Analysis of DataSet GSE117769
GONÇALVES, L.C.
2025-10-27
1. Installing and Loading Packages
This first block of code installs and loads all the libraries needed
for the analysis. The include=FALSE option in the block
header ensures that the installation commands and loading messages will
not appear in the final HTML report, making it cleaner.
2. Data Loading and Preparation
Here, we load the raw count table and gene annotations directly from the GEO repository.
# load counts table from GEO
urld <- "https://www.ncbi.nlm.nih.gov/geo/download/?format=file&type=rnaseq_counts"
path <- paste(urld, "acc=GSE117769", "file=GSE117769_raw_counts_GRCh38.p13_NCBI.tsv.gz", sep="&");
gset<- as.matrix(data.table::fread(path, header=T, colClasses="integer"), rownames="GeneID")
# load gene annotations
apath <- paste(urld, "type=rnaseq_counts", "file=Human.GRCh38.p13.annot.tsv.gz", sep="&")
annot <- data.table::fread(apath, header=T, quote="", stringsAsFactors=F, data.table=F)
# Load the dataset
gse <- getGEO("GSE117769", GSEMatrix = TRUE, AnnotGPL = TRUE)## Found 1 file(s)## GSE117769_series_matrix.txt.gz## Annotation GPL not available, so will use submitter GPL insteadgse <- gse[[1]]
# Extract phenotype data
pheno_data <- pData(gse)
pheno_data <- pheno_data[, c("title", "geo_accession", "characteristics_ch1.6")]3. Selection of 433 genes
Gene selection performed by text mining and functional enrichment.
#Define genes of interest
genes_of_interest <- c(
"ABCB11", "ABCD2", "ACE", "ACKR2", "ACP5", "ACP7", "ADAMTS9", "ADCY7", "ADGRL2", "ADIPOQ", "AHR", "AIM2", "AKAP13", "ALB", "ANKRD55", "ANXA1",
"APOL1", "APOL6", "AQP1", "AREG", "ARHGEF3", "ATG16L1", "ATG5", "ATOX1", "ATXN2L", "BEND2", "BGLAP", "BMP2", "BMP7", "BNIP3L", "BRAF", "BTG1",
"C15ORF48", "C7ORF57", "CALD1", "CAPS2", "CARD9", "CASP1", "CASP10", "CAST", "CCL2", "CCL20", "CCL25", "CCL3", "CCL5", "CCND1", "CCND3", "CCR2",
"CCR6", "CCR7", "CCRL2", "CD14", "CD160", "CD19", "CD274", "CD28", "CD36", "CD38", "CD3E", "CD4", "CD40", "CD40LG", "CD52", "CD63", "CD68",
"CD69", "CD80", "CD83", "CD86", "CD8A", "CD8B", "CDC42BPB", "CEBPA", "CEBPG", "CENPK", "CLEC2B", "CLEC4D", "CLIC3", "CMAHP", "CMTM2",
"COL1A1", "COX2", "CRB1", "CREM", "CRP", "CSF2", "CSMD1", "CSN3", "CSNK1A1", "CTLA4", "CTSB", "CTSK", "CUX1", "CX3CR1", "CXCL10", "CXCL13",
"CXCL16", "CXCL2", "CXCL8", "CXCR2", "CYCS", "CYP1A1", "CYP4F22", "DDIT3", "DDX60", "DKK1", "DLAT", "DNAJA2", "DNAJB6", "DUSP4", "DYSF",
"EDNRA", "EFCAB13", "EFCAB7", "EGF", "EGFR", "EGR3", "EIF5B", "ENO1", "EOMES", "ERAP1", "ERAP2", "ERN1", "ERP44", "EZH2", "FAXDC2", "FCGR1A",
"FCGR2A", "FCGR3A", "FGB", "FNBP1", "FOS", "FOSL1", "FOSL2", "FOXP3", "FRZB", "FUT2", "GAPDH", "GATA3", "GBP1", "GBP3", "GBP5", "GEM", "GINS1",
"GJB2", "GJB6", "GLUL", "GOLIM4", "GPR35", "GPT", "GZMA", "GZMB", "GZMK", "HCAR3", "HERC6", "HHAT", "HIF1A", "HK2", "HLA-A", "HLA-B", "HLA-C",
"HLA-DQB1", "HLA-DRB1", "HSPA5", "HSPA6", "HYAL4", "ICAM1", "ICOS", "IFI16", "IFI6", "IFIH1", "IFIT3", "IFNA1", "IFNG", "IFNGR1", "IFNLR1",
"IGF2", "IGF2-AS", "IL10", "IL12B", "IL13", "IL15", "IL17A", "IL17F", "IL17RA", "IL18", "IL1A", "IL1B", "IL1F10", "IL1R1", "IL1RN", "IL2",
"IL21", "IL21-AS1", "IL22", "IL23A", "IL23R", "IL2RA", "IL33", "IL36RN", "IL37", "IL4", "IL5", "IL6", "IL6R", "IL7", "INS", "INS-IGF2", "IRAK1",
"IRS1", "ITGA2B", "ITGAL", "ITGAM", "ITGAX", "JAK2", "JAK3", "JDP2", "JRKL", "JUN", "JUNB", "JUND", "KANK4", "KDM5B", "KIR2DS1", "KIR3DL1",
"KIR3DL2", "KLRB1", "LAMP1", "LAMP2", "LEP", "LILRA5", "LILRB2", "LINC01185", "LINC01250", "LMO7", "LPAL2", "LRRK2", "LTA", "LURAP1L",
"LURAP1L-AS1", "LYZ", "MAF", "MBL2", "MCAM", "MCL1", "MEFV", "MICA", "MIR146A", "MIR21", "MIX23", "MMP1", "MMP3", "MMP7", "MMP9", "MRPS23",
"MSN", "MTHFR", "MUCL1", "MX1", "MYC", "MYNN", "NABP1", "NAMPT", "NCOA7", "NDUFS1", "NFKB1", "NKG7", "NLRP3", "NMI", "NOD2", "NOS2",
"NOXRED1", "NPEPPS", "NRG1", "NT5C3A", "OLR1", "OSMR", "PDCD1", "PDLIM7", "PER1", "PFDN4", "PFDN5", "PFKL", "PGD", "PGK1", "PHEX", "PI3",
"PIK3CD", "PINK1", "PLA2G4D", "PLCG1", "PLG", "PLIN5", "PLS1", "PPARD", "PPARG", "PPARGC1A", "PPARGC1B", "PRDM1", "PRF1", "PRTN3", "PSG2",
"PSMC2", "PSMD7", "PSME2", "PTGS1", "PTGS2", "PTH", "PTPN22", "PTX3", "PYGL", "RAC1", "RBM45", "REL", "RETN", "RGPD6", "RIT1", "RORC", "RPL15",
"RPL36AL", "RPL41", "RPL7", "RPS19", "RPS21", "RPS26", "RPS6KB1", "RPS7", "RSAD2", "RUNX2", "RUNX3", "S100A12", "S100A8", "S100A9", "S100P",
"SAA1", "SAMD9", "SAR1A", "SCN1A", "SEC14L2", "SEC24B", "SELL", "SERPINA1", "SERPINB1", "SERPINE1", "SF3B1", "SF3B3", "SGK1", "SH3BGRL3",
"SIAH1", "SLC1A2", "SLC2A3", "SLC51B", "SLC7A11", "SLC7A5", "SMAD3", "SMARCA4", "SMOX", "SOCS1", "SOD2", "SOST", "SOX4", "SP7", "SPCS3",
"SPON2", "SPP1", "SSR1", "STAT1", "STAT3", "STIM1", "SUOX", "SYT1", "TALDO1", "TBX21", "TEK", "TFPI", "TGFA", "TGFB1", "TGFBR3", "TIMP1",
"TLR2", "TLR3", "TLR4", "TLR9", "TMBIM6", "TMEM45A", "TMPRSS11B", "TNF", "TNFAIP3", "TNFAIP6", "TNFAIP8", "TNFRSF10A", "TNFRSF1A",
"TNFRSF1B", "TNFRSF9", "TNFSF10", "TNFSF11", "TNFSF13B", "TNFSF15", "TNIP1", "TOMM5", "TOMM7", "TPST2", "TPT1", "TRAF2", "TRAF3IP2", "TRAF4",
"TRAF5", "TRBV20OR9-2", "TRIM22", "TRIM69", "TTC39B", "TYK2", "TYMP", "UBE2L3", "UQCR10", "UTP11", "VCAM1", "VDR", "VEGFA", "VIM", "WDR1",
"WNK1", "WWOX", "XAF1", "XBP1", "YOD1", "YWHAB", "ZC3H12A", "ZFP36", "ZMIZ1", "ZNF316", "ZNF415", "ZNF483"
)
# Load the data.table package
library(data.table)
# Keep only the notes for the genes of interest.
annot_filtered <- annot[annot$Symbol %in% genes_of_interest, ]
# Filter the count matrix using GeneIDs as the key (MUCH MORE SECURE)
expr_data_filtered <- gset[rownames(gset) %in% annot_filtered$GeneID, ]
# Filter expression data for genes of interest
express <- rownames(expr_data_filtered)
# Mapping Entrez IDs to gene symbols
gene_symbols <- mapIds(org.Hs.eg.db, keys = rownames(expr_data_filtered), column = "SYMBOL", keytype = "ENTREZID", multiVals = "first")## 'select()' returned 1:1 mapping between keys and columns# Replace rownames with gene symbols
rownames(expr_data_filtered) <- gene_symbols
# View the updated dataframe
print("Data frame com rownames modificados para símbolos de genes:")## [1] "Data frame com rownames modificados para símbolos de genes:"print(expr_data_filtered)## GSM3308425 GSM3308426 GSM3308427 GSM3308428 GSM3308429 GSM3308430
## TNFRSF9 215 150 89 176 100 125
## ENO1 7327 8128 5485 6627 5161 7547
## PIK3CD 7748 6895 5701 5781 7085 7138
## PGD 8407 6039 3905 5438 5479 4306
## MTHFR 398 445 514 232 304 520
## TNFRSF1B 18991 14198 10710 13867 16404 12864
## PINK1 955 767 575 675 818 757
## IFNLR1 19 51 92 32 36 68
## RUNX3 1322 4550 5169 3042 2378 4679
## SH3BGRL3 11632 12131 9679 11733 10451 10061
## CD52 3566 5289 5744 4952 3982 5456
## IFI6 3133 1475 772 1568 809 730
## ZC3H12A 491 619 548 764 620 505
## UTP11 109 138 105 100 87 149
## JUN 1862 8233 8148 5007 5830 10406
## KANK4 1 0 0 0 0 0
## EFCAB7 12 32 42 26 19 41
## IL23R 0 0 9 0 1 4
## ADGRL2 0 0 2 0 0 0
## GBP3 112 99 152 225 123 97
## GBP1 4776 1250 708 1063 973 1330
## GBP5 16798 3645 2287 3083 2607 4404
## TGFBR3 108 964 1316 565 436 853
## VCAM1 0 1 10 0 2 2
## PTPN22 254 530 560 252 286 393
## CD160 12 238 246 119 139 158
## FCGR1A 4251 1170 436 941 512 1004
## MCL1 31572 23108 24285 23989 25605 23964
## CTSK 82 43 72 95 69 56
## RORC 23 20 78 13 30 139
## S100A9 174389 136992 72218 166968 160609 82813
## S100A12 4290 4083 2316 5337 3979 2054
## S100A8 70275 52729 28270 65639 65588 31098
## IL6R 5039 3544 2457 3368 4563 3440
## RIT1 1582 1320 1056 1503 1592 1205
## BGLAP 9 6 4 10 5 11
## IFI16 5627 3628 2121 2337 2596 3160
## AIM2 427 143 109 66 126 123
## CRP 0 0 0 0 0 0
## FCGR2A 19096 14203 5545 10872 12557 11696
## HSPA6 3042 1929 1473 1952 2779 1769
## FCGR3A 27658 15736 17102 10001 19051 15848
## SELL 41683 31311 18369 30083 26582 28922
## GLUL 22808 15924 12630 18063 22910 13895
## PTGS2 17440 9183 3896 6214 7372 12501
## CRB1 0 0 0 0 2 2
## KDM5B 434 347 379 444 452 367
## IL10 5 7 4 4 4 11
## YOD1 242 325 442 291 283 240
## HHAT 17 41 54 16 35 56
## TRAF5 118 271 501 199 235 495
## NLRP3 1004 1092 606 566 522 898
## LINC01250 0 0 0 0 0 0
## RPS7 4213 8270 10963 9575 9055 10458
## RSAD2 2276 540 292 400 279 274
## FOSL2 3834 4660 4475 3545 4234 3851
## REL 1001 991 1067 670 679 1070
## TGFA 740 558 441 533 915 500
## DYSF 7777 4904 2078 4396 3539 3418
## HK2 1436 923 609 1000 1017 662
## CD8A 376 4290 2596 1188 1210 1667
## CD8B 242 1281 1170 684 552 577
## EIF5B 337 541 697 377 400 620
## IL1R1 164 285 211 241 234 190
## RGPD6 44 67 96 56 70 67
## IL1A 1 1 0 0 0 0
## IL1B 929 1268 271 344 442 857
## IL37 0 0 1 0 0 0
## IL36RN 0 0 0 0 0 0
## IL1F10 0 0 0 0 0 0
## IL1RN 3426 3307 1562 2129 2788 1781
## NMI 3119 860 1191 1840 1856 1810
## TNFAIP6 777 489 319 294 482 321
## IFIH1 965 450 377 389 359 439
## SCN1A 0 0 0 0 0 0
## ABCB11 2 0 0 0 0 0
## RBM45 45 66 54 33 50 45
## FRZB 0 1 1 0 0 0
## TFPI 5 3 5 6 7 4
## STAT1 12808 5503 3057 5044 4313 5156
## NABP1 1002 778 474 533 659 692
## SF3B1 4388 4817 5085 3899 3730 4362
## CASP10 342 345 384 296 257 411
## CD28 147 383 915 397 623 814
## CTLA4 22 62 111 87 88 52
## ICOS 45 144 160 89 111 135
## NDUFS1 594 585 522 485 456 566
## CXCR2 25851 19265 13203 16164 19481 19491
## IRS1 25 50 79 23 41 42
## CCL20 2 3 3 1 0 4
## ATG16L1 209 368 488 358 264 360
## GPR35 82 161 142 191 85 102
## PDCD1 16 57 24 20 35 92
## PPARG 4 5 1 3 0 3
## RPL15 8125 13815 16171 13979 11672 16183
## EOMES 34 232 228 121 148 267
## CX3CR1 1228 1438 585 650 541 1451
## ACKR2 1 0 1 1 1 5
## CCR2 931 1139 394 183 230 775
## CCRL2 66 39 41 28 43 27
## TLR9 88 64 57 57 64 74
## ARHGEF3 663 1355 1445 880 906 1486
## ADAMTS9 0 0 0 0 0 0
## TMEM45A 0 0 1 4 1 2
## CD80 2 5 5 4 4 2
## CD86 1198 1213 892 728 625 752
## MIX23 10 30 31 15 24 34
## PLS1 11 9 21 7 11 16
## PTX3 35 75 30 43 21 41
## GOLIM4 100 137 85 43 55 118
## MYNN 293 303 431 363 344 356
## TNFSF10 8062 3623 1996 2513 2958 3160
## ADIPOQ 0 0 0 0 0 0
## SPON2 130 587 365 623 410 936
## S100P 4031 1643 3078 4653 6224 3577
## WDR1 6832 6470 5499 5291 5797 6608
## CD38 189 252 208 216 188 428
## PPARGC1A 7 14 0 0 1 3
## TMPRSS11B 0 0 0 0 0 0
## CSN3 0 0 0 0 0 0
## ALB 0 0 0 0 1 0
## CXCL8 14269 40868 27037 49181 62059 38786
## CXCL2 13 8 5 6 7 17
## AREG 124 37 148 55 17 56
## CXCL10 87 42 20 24 7 22
## CXCL13 0 0 0 0 0 0
## SPP1 52 35 65 27 82 33
## HERC6 198 187 196 142 138 201
## NFKB1 1056 1020 818 779 696 879
## SEC24B 497 429 509 412 358 458
## EGF 31 32 32 23 34 22
## IL2 0 0 0 0 1 1
## IL21 0 1 3 1 1 0
## IL21-AS1 0 0 1 0 2 3
## SLC7A11 6 5 7 11 9 4
## IL15 112 132 92 65 55 90
## EDNRA 0 0 0 0 0 0
## TLR2 4647 3301 2210 2985 2499 3111
## FGB 0 0 0 0 0 0
## DDX60 1097 378 366 318 255 450
## SPCS3 1900 2307 2088 1707 1813 2122
## TLR3 3 17 14 5 5 20
## OSMR 28 24 30 27 15 20
## GZMK 132 757 1470 386 850 1341
## GZMA 243 2116 2025 924 992 1765
## ANKRD55 51 48 60 67 33 72
## CENPK 15 43 182 21 59 131
## CAST 2814 3256 2812 2159 2006 2532
## ERAP1 1792 1172 1192 995 1042 1443
## ERAP2 1388 1738 296 1112 1095 1712
## TNFAIP8 838 1146 1599 934 1268 1670
## CSF2 0 0 0 0 0 3
## IL5 0 0 0 1 1 2
## IL13 0 1 0 0 0 2
## IL4 2 0 4 0 0 13
## CD14 8936 11140 3631 5765 6288 6189
## CSNK1A1 2002 1771 1448 1549 1457 1763
## PPARGC1B 166 132 126 105 70 115
## TNIP1 5014 4601 4153 4274 4632 4277
## ATOX1 222 253 158 184 175 187
## FAXDC2 162 181 215 194 170 160
## IL12B 0 1 0 0 0 1
## MIR146A 0 0 0 0 0 0
## PDLIM7 2170 1996 932 2155 2278 1386
## SERPINB1 5640 5571 3193 5230 4743 4111
## SSR1 2456 2751 2145 1944 2072 2257
## CD83 539 424 411 348 272 596
## SOX4 175 296 192 277 192 226
## CMAHP 81 75 100 73 59 96
## HLA-A 63666 51852 38228 49718 39870 42463
## HLA-C 77198 64852 44225 64328 61196 91472
## HLA-B 144517 110030 75162 120772 105472 103482
## MICA 150 125 181 130 158 255
## LTA 19 52 55 40 57 84
## TNF 124 396 145 212 146 130
## HLA-DRB1 4013 6062 2940 3633 2690 4398
## HLA-DQB1 421 730 511 3011 471 339
## PPARD 212 295 361 267 244 345
## CCND3 4059 4088 3609 4303 3339 4415
## VEGFA 221 199 170 171 208 184
## RUNX2 413 391 684 517 509 633
## IL17A 0 0 1 0 1 1
## IL17F 0 0 0 0 0 0
## PRDM1 552 686 861 425 358 772
## ATG5 362 471 486 444 423 414
## TRAF3IP2 112 197 224 191 157 233
## NCOA7 274 339 388 246 205 367
## SGK1 2736 2853 1787 1268 1734 2852
## IFNGR1 3696 2747 2280 3258 3068 2430
## TNFAIP3 2504 4237 7423 3954 2578 6491
## SOD2 55745 43148 31809 42424 48515 38883
## LPAL2 15 23 29 6 11 31
## PLG 0 1 1 0 0 1
## CCR6 38 65 147 45 51 154
## RAC1 3199 2939 2654 3384 2948 3072
## ZNF316 741 871 612 867 643 735
## AHR 855 1037 911 790 551 830
## IL6 7 1 9 4 5 4
## TOMM7 1236 2316 2599 1938 2415 2340
## CYCS 476 704 737 489 501 639
## AQP1 1 1 5 3 3 3
## NT5C3A 1283 713 655 779 886 654
## EGFR 0 0 0 0 0 0
## CD36 2569 3426 2019 2503 1700 1706
## SAMD9 2688 1475 1234 1144 1270 1829
## SERPINE1 9 5 11 10 2 10
## CUX1 1898 1678 1193 1393 1197 1367
## PSMC2 417 443 393 353 295 431
## NAMPT 64627 44963 31465 55150 59765 32702
## HYAL4 0 0 0 0 0 0
## LEP 4 2 6 0 11 2
## CALD1 15 12 19 20 14 12
## BRAF 645 620 708 520 560 654
## EZH2 51 58 68 52 41 65
## DNAJB6 1668 1697 1420 1651 1658 1629
## CSMD1 3 2 5 2 22 15
## CTSB 5895 8342 4744 4399 3285 5854
## EGR3 561 535 152 133 226 525
## TNFRSF10A 79 144 186 92 144 203
## BNIP3L 3065 2541 1918 2502 2693 2158
## DUSP4 33 58 90 51 46 42
## NRG1 65 94 119 87 24 69
## RPL7 5539 9433 13219 9822 9278 11239
## IL7 10 12 21 6 10 6
## GEM 1 2 0 0 0 0
## MYC 248 470 615 272 349 571
## GPT 1 1 4 2 0 3
## JAK2 1605 1207 885 837 726 871
## CD274 583 180 136 123 131 170
## IL33 0 0 1 0 0 0
## LURAP1L-AS1 0 0 0 0 0 0
## LURAP1L 1 1 3 0 2 2
## TTC39B 43 102 246 107 123 169
## IFNA1 0 0 0 0 0 0
## TEK 3 23 9 28 11 25
## TRBV20OR9-2 0 0 0 0 0 0
## TOMM5 152 249 303 214 187 261
## ANXA1 7075 8806 8672 4819 5084 6858
## ERP44 1908 1627 1280 1471 1423 1442
## ZNF483 7 29 67 30 28 32
## TNFSF15 15 12 3 4 4 7
## TLR4 6050 6015 3130 3539 4990 4282
## PTGS1 656 761 808 899 883 645
## HSPA5 8341 6043 5967 6311 5315 7816
## FNBP1 3491 3751 3312 3027 2889 3946
## CARD9 230 240 122 201 175 212
## TRAF2 85 124 133 109 113 165
## CLIC3 37 171 93 113 150 184
## IL2RA 36 109 146 46 104 161
## GATA3 182 314 369 173 235 759
## VIM 17694 20339 14684 15966 15704 15250
## CREM 124 199 223 165 174 155
## DKK1 0 0 0 0 0 0
## MBL2 0 0 0 0 0 0
## SAR1A 950 913 931 1032 1008 864
## PRF1 633 4208 2491 2309 2032 5638
## ZMIZ1 2134 2089 1474 1646 1855 1951
## IFIT3 15574 3582 2244 5208 3603 3734
## TALDO1 13747 9895 6189 11167 11394 9044
## IGF2 0 0 1 0 0 1
## INS-IGF2 0 0 1 0 0 1
## IGF2-AS 0 0 0 0 0 0
## INS 0 0 0 0 0 0
## STIM1 958 1425 1279 1070 1028 1400
## TRIM22 7247 3165 2129 2409 1823 2737
## PTH 0 0 0 0 0 0
## SAA1 0 0 0 0 0 0
## SLC1A2 0 1 2 1 1 0
## FOSL1 27 71 31 25 14 24
## CCND1 9 14 13 9 5 10
## JRKL 56 106 119 34 51 131
## MMP7 0 0 1 0 0 0
## MMP1 1 2 0 0 3 1
## MMP3 0 0 0 0 0 0
## CASP1 5164 3626 2507 3255 2716 2798
## DLAT 146 202 181 121 136 241
## IL18 140 117 109 131 110 91
## CD3E 819 3501 4859 2455 2525 4247
## MCAM 224 202 293 319 253 215
## WNK1 3515 3372 2894 2514 2523 4125
## TNFRSF1A 4776 4292 2064 2651 3211 3784
## GAPDH 18364 20325 14369 20383 17159 16477
## CD4 4852 5099 4702 3482 3019 5464
## SLC2A3 12157 11814 7369 9333 6787 7040
## CLEC4D 693 393 378 340 461 176
## KLRB1 197 870 1719 552 863 1018
## CD69 1250 2002 3406 1603 1551 3425
## CLEC2B 2659 2155 1565 2384 2491 1798
## OLR1 27 14 1 7 7 8
## ABCD2 37 133 200 106 136 194
## LRRK2 10976 6561 5864 7272 8997 5226
## VDR 494 373 359 325 432 343
## TMBIM6 13633 14761 11614 11271 12182 13938
## PFDN5 2700 3443 3998 3975 3085 3735
## SP7 0 0 0 0 0 0
## MUCL1 0 0 0 0 0 0
## CD63 3912 3028 2583 3587 3023 2705
## SUOX 1367 1156 1038 1055 1168 1166
## RPS26 700 3521 8158 7028 6366 7913
## RPL41 4112 7190 9312 8336 7835 9293
## IL23A 25 33 56 41 43 54
## DDIT3 816 636 706 951 988 801
## IFNG 5 95 131 57 30 60
## IL22 0 0 0 0 0 1
## LYZ 86438 63027 51809 108771 71035 51896
## CAPS2 1 8 5 1 7 4
## SYT1 1 5 14 2 1 1
## BTG1 9786 9904 14778 11213 11795 13904
## HCAR3 2829 2540 1410 1819 1654 2431
## GJB2 1 1 1 1 2 2
## GJB6 22 33 22 15 39 20
## TNFSF11 1 0 7 0 2 3
## TPT1 33506 54642 66433 58762 56759 59660
## LMO7 17 37 83 48 37 97
## TNFSF13B 3009 2754 2092 2068 2321 1868
## LAMP1 3199 3480 2443 2702 2885 2961
## PSME2 2820 1839 1370 1939 1338 1642
## GZMB 311 1513 1456 975 646 1396
## RPL36AL 2060 2164 2157 2305 2305 2706
## PYGL 7954 5644 2643 5638 5824 4177
## HIF1A 2548 2451 1881 2918 3103 1667
## FOS 22296 46740 46884 50308 46684 40941
## JDP2 893 778 602 999 886 661
## NOXRED1 9 13 18 8 4 10
## SERPINA1 30483 27122 16661 28980 23113 17589
## CDC42BPB 239 307 209 167 139 257
## PLA2G4D 0 0 0 0 0 0
## TRIM69 20 21 21 11 21 25
## SLC51B 0 0 0 0 0 0
## SMAD3 373 618 880 478 467 712
## CYP1A1 2 1 0 1 0 0
## AKAP13 4672 4069 3682 2832 3057 3829
## MEFV 4464 2667 1996 2557 2558 2739
## SOCS1 87 70 61 45 55 112
## ATXN2L 1441 1989 2085 1503 1366 2323
## CD19 54 93 249 86 101 192
## ITGAL 5285 6069 5437 4464 3930 6665
## ITGAM 5837 5829 3620 4250 4439 4481
## ITGAX 6098 5958 4423 6019 5664 4730
## DNAJA2 817 636 650 653 615 806
## SIAH1 92 121 156 151 126 137
## ADCY7 2527 2890 2493 1475 1580 3002
## NOD2 2611 1020 727 1424 1387 443
## CMTM2 2942 2112 1344 2640 3024 2420
## SF3B3 691 1003 932 563 616 1247
## PSMD7 712 774 748 815 763 731
## WWOX 24 49 49 28 33 80
## MAF 263 692 582 263 358 623
## SLC7A5 119 318 260 211 284 368
## CXCL16 3836 1863 1634 1885 1956 2012
## XAF1 2581 992 974 715 676 992
## CD68 6129 5489 3499 4534 3340 4151
## PER1 622 602 1037 1246 572 688
## NOS2 3 0 2 1 0 0
## TRAF4 42 97 138 82 91 147
## CCL2 0 7 17 1 0 5
## CCL5 967 8243 8874 4226 3564 4951
## CCL3 238 338 268 173 178 507
## CCR7 107 381 522 380 424 715
## STAT3 7265 5104 3581 4240 4560 5042
## SOST 0 0 0 0 0 0
## ITGA2B 414 365 360 753 699 256
## EFCAB13 11 15 45 16 12 13
## NPEPPS 1016 903 702 839 879 838
## TBX21 76 653 601 367 356 612
## COL1A1 3 0 0 1 4 0
## MRPS23 166 205 165 143 118 215
## MIR21 5 9 1 7 8 9
## RPS6KB1 263 361 427 247 301 373
## ACE 25 28 61 21 26 106
## ERN1 830 1070 1420 682 903 1588
## PRTN3 40 13 1 29 2 17
## PLIN5 155 142 57 106 153 113
## RETN 83 68 44 131 59 47
## CCL25 0 0 0 1 1 0
## ICAM1 2565 2254 1197 1763 1775 1718
## TYK2 1892 2173 1624 1734 1868 1962
## SMARCA4 620 793 670 530 556 918
## ACP5 259 284 257 228 229 278
## JUNB 26574 50077 18954 54780 52521 32132
## CYP4F22 94 48 33 52 21 29
## JAK3 2057 2357 2028 2083 1943 2213
## JUND 4808 8639 5258 8393 10077 7967
## CEBPA 1241 1214 574 1091 1024 776
## CEBPG 263 317 356 321 245 334
## ACP7 0 0 0 0 2 7
## ZFP36 18624 32508 17164 31390 29263 22637
## TGFB1 6072 7008 3890 5572 5253 5468
## RPS19 5643 9974 12585 10710 10270 12916
## PSG2 0 0 0 0 0 0
## FUT2 1 1 9 4 4 1
## NKG7 804 6553 5829 4062 3155 5383
## ZNF415 3 2 9 4 3 17
## LILRB2 7068 5564 3714 4917 4793 4073
## LILRA5 4604 3943 1474 3242 3981 2642
## KIR3DL1 31 61 53 28 52 75
## KIR3DL2 6 32 102 63 31 151
## SMOX 92 111 135 147 118 123
## BMP2 3 7 3 5 0 5
## GINS1 2 8 10 3 6 6
## PLCG1 220 749 1047 408 470 1031
## YWHAB 6224 7104 5424 5476 5783 6340
## PI3 3948 1928 292 1311 156 579
## MMP9 4194 2848 667 3176 4200 1463
## CD40 334 247 137 131 125 182
## PFDN4 30 62 75 46 45 55
## BMP7 0 0 0 0 0 0
## RPS21 2176 4277 5294 5211 5025 6179
## MX1 3252 1337 1153 836 776 808
## PFKL 1220 1377 938 968 834 1347
## IL17RA 7894 5359 3566 4887 5020 4533
## UBE2L3 1131 1179 1084 1007 902 1159
## TPST2 1023 1545 1300 1184 1017 1408
## XBP1 940 1234 1336 1152 1133 1254
## UQCR10 550 647 581 549 555 614
## SEC14L2 11 20 41 28 19 36
## APOL6 4173 1696 1351 1213 1218 1954
## APOL1 2322 834 510 725 799 783
## TYMP 7482 4155 2260 4360 3942 2634
## BEND2 39 42 109 59 37 49
## PHEX 11 5 20 4 6 10
## TIMP1 1392 1803 1480 1068 1239 1909
## FOXP3 42 69 75 52 76 77
## MSN 30304 25333 20651 21752 20890 26501
## PGK1 9900 8842 7120 7263 6756 7591
## LAMP2 8221 6466 5529 6588 8014 6131
## CD40LG 51 153 253 110 141 298
## IRAK1 1332 1730 1456 1265 1208 1599
## COX2 39992 63303 80860 61595 46396 56578
## GSM3308431 GSM3308432 GSM3308433 GSM3308434 GSM3308435 GSM3308436
## TNFRSF9 101 166 150 104 51 131
## ENO1 6629 5839 6206 6010 5729 5522
## PIK3CD 6976 6348 7702 4977 5417 4844
## PGD 4600 6740 5903 4435 4610 4058
## MTHFR 564 389 518 325 393 356
## TNFRSF1B 15464 14056 13732 11344 12920 10709
## PINK1 788 899 941 540 747 440
## IFNLR1 63 38 66 36 16 48
## RUNX3 4118 3755 2697 3697 3916 4408
## SH3BGRL3 10348 11997 9956 10343 11600 9212
## CD52 4626 2991 4278 5631 4359 4253
## IFI6 786 1952 637 1824 736 508
## ZC3H12A 693 649 453 877 931 995
## UTP11 120 101 116 96 79 83
## JUN 6838 3488 6866 6561 7894 10311
## KANK4 1 0 0 1 0 0
## EFCAB7 46 20 23 17 18 19
## IL23R 2 3 0 0 2 4
## ADGRL2 0 0 0 0 0 0
## GBP3 140 282 274 68 138 53
## GBP1 784 1612 1066 557 286 274
## GBP5 2472 4959 2426 2235 1469 1040
## TGFBR3 763 746 401 716 679 1048
## VCAM1 1 7 5 2 0 5
## PTPN22 435 341 398 281 211 316
## CD160 185 143 101 94 64 119
## FCGR1A 356 1095 480 503 212 221
## MCL1 24197 28918 28200 28445 27742 18408
## CTSK 75 43 107 114 48 61
## RORC 50 13 52 3 29 32
## S100A9 102836 152151 119272 117422 112214 89816
## S100A12 2196 3795 3050 2968 2851 2919
## S100A8 38048 57591 45633 43499 40319 35386
## IL6R 3780 4370 4678 2168 2761 2580
## RIT1 1224 1557 1317 1843 2188 1125
## BGLAP 8 7 11 4 6 5
## IFI16 2416 3110 2286 1475 1138 1235
## AIM2 77 133 145 77 62 60
## CRP 0 0 0 0 0 0
## FCGR2A 11960 12686 11761 8604 8778 7547
## HSPA6 2166 2633 1651 1090 1203 1184
## FCGR3A 16626 18954 16955 13357 12839 7845
## SELL 20647 36638 22564 25233 26124 17290
## GLUL 16203 16555 16667 15936 17411 13566
## PTGS2 3227 7759 14738 2393 2136 2222
## CRB1 4 1 2 0 2 1
## KDM5B 400 418 439 404 489 313
## IL10 1 1 6 9 1 3
## YOD1 359 274 280 434 452 413
## HHAT 50 34 34 36 40 45
## TRAF5 428 221 319 187 255 200
## NLRP3 601 1003 974 1319 905 693
## LINC01250 1 0 0 0 0 1
## RPS7 10714 7513 7126 8961 9520 8473
## RSAD2 252 860 191 446 123 62
## FOSL2 4114 4425 3971 4120 4396 5376
## REL 1015 680 886 1158 1141 833
## TGFA 652 466 549 336 418 500
## DYSF 2632 5472 3552 2570 2732 2431
## HK2 846 906 1179 811 662 631
## CD8A 1954 2449 955 1563 1166 2337
## CD8B 865 1094 461 698 436 501
## EIF5B 535 364 524 310 325 337
## IL1R1 199 215 301 243 305 201
## RGPD6 98 62 66 62 60 46
## IL1A 0 0 1 0 0 0
## IL1B 332 550 497 227 254 515
## IL37 0 0 0 0 0 0
## IL36RN 0 0 0 0 0 0
## IL1F10 0 0 0 0 0 0
## IL1RN 2087 2030 1913 1794 1788 3204
## NMI 1532 1716 1493 996 897 740
## TNFAIP6 365 627 223 180 131 178
## IFIH1 390 499 261 300 241 206
## SCN1A 0 0 0 0 0 0
## ABCB11 2 2 1 1 3 0
## RBM45 62 46 49 54 34 35
## FRZB 0 0 1 0 1 0
## TFPI 3 8 2 7 12 3
## STAT1 3429 5941 3804 2945 2175 1710
## NABP1 628 666 817 402 469 451
## SF3B1 4811 4217 5263 4215 4661 3772
## CASP10 359 252 413 271 294 254
## CD28 764 339 590 471 623 426
## CTLA4 93 42 71 86 94 78
## ICOS 141 106 112 114 98 96
## NDUFS1 501 477 552 373 424 346
## CXCR2 17011 20829 17760 8991 10545 8457
## IRS1 82 29 91 23 32 55
## CCL20 2 1 1 1 2 3
## ATG16L1 395 281 298 332 348 321
## GPR35 130 93 143 167 291 196
## PDCD1 40 35 30 18 23 30
## PPARG 1 5 0 12 3 5
## RPL15 15321 11640 12182 13420 14096 11956
## EOMES 178 204 114 92 86 156
## CX3CR1 657 736 1042 252 181 554
## ACKR2 1 3 2 1 3 1
## CCR2 354 483 523 218 178 226
## CCRL2 27 61 40 42 29 26
## TLR9 57 68 123 47 57 64
## ARHGEF3 1263 926 882 836 931 927
## ADAMTS9 0 1 0 0 0 0
## TMEM45A 5 2 1 5 1 1
## CD80 8 3 14 3 5 5
## CD86 781 909 896 640 582 480
## MIX23 31 20 30 23 21 14
## PLS1 10 16 18 7 14 9
## PTX3 36 84 57 79 70 55
## GOLIM4 75 98 95 57 60 71
## MYNN 307 269 366 359 403 298
## TNFSF10 2596 4064 2958 1562 1444 1064
## ADIPOQ 0 0 0 0 0 0
## SPON2 661 333 523 589 278 1191
## S100P 3546 2784 5359 3731 2223 1712
## WDR1 6084 6371 6357 4631 5057 4616
## CD38 258 130 459 185 124 240
## PPARGC1A 5 3 8 0 12 1
## TMPRSS11B 0 0 0 0 0 0
## CSN3 0 0 0 0 0 0
## ALB 0 0 0 0 0 2
## CXCL8 30976 25086 35808 32430 58462 32299
## CXCL2 3 18 10 7 16 8
## AREG 21 82 27 315 228 104
## CXCL10 11 36 35 5 3 6
## CXCL13 0 0 0 0 0 0
## SPP1 62 121 30 38 80 104
## HERC6 139 223 174 98 160 90
## NFKB1 774 786 779 785 726 614
## SEC24B 482 397 466 422 569 370
## EGF 45 42 16 37 51 18
## IL2 0 0 0 1 1 1
## IL21 0 0 0 0 0 1
## IL21-AS1 1 0 1 0 0 0
## SLC7A11 10 6 12 10 18 4
## IL15 77 83 80 65 46 39
## EDNRA 1 0 0 0 0 0
## TLR2 2469 3594 3201 3108 4051 1955
## FGB 0 0 0 0 0 0
## DDX60 269 420 278 284 167 156
## SPCS3 1757 1932 2295 1529 1598 1582
## TLR3 13 4 10 4 9 18
## OSMR 26 27 24 32 39 24
## GZMK 1157 1618 621 482 579 545
## GZMA 1305 1430 835 867 792 1344
## ANKRD55 38 39 85 60 35 44
## CENPK 67 88 95 10 56 68
## CAST 2700 2587 2238 2609 2944 1867
## ERAP1 1335 1036 1187 1666 1497 761
## ERAP2 1524 2459 2503 1168 1009 130
## TNFAIP8 1502 972 1278 913 900 890
## CSF2 0 1 0 1 0 0
## IL5 0 1 0 0 1 0
## IL13 1 1 0 0 2 0
## IL4 5 2 0 7 0 1
## CD14 5911 6682 8226 5243 4547 5879
## CSNK1A1 1363 1585 1628 1303 1269 984
## PPARGC1B 153 75 107 193 150 99
## TNIP1 4863 4998 4771 3528 4253 4346
## ATOX1 172 204 180 199 198 245
## FAXDC2 229 176 150 133 251 129
## IL12B 0 2 1 0 1 1
## MIR146A 0 0 1 0 1 1
## PDLIM7 1944 2158 2260 1582 2079 1769
## SERPINB1 4102 4014 3331 3827 3672 3311
## SSR1 2170 2392 2544 1861 2034 1600
## CD83 301 551 622 752 443 485
## SOX4 267 107 155 242 396 227
## CMAHP 103 63 72 63 65 61
## HLA-A 39142 59096 53261 51438 32838 33649
## HLA-C 52883 67491 83964 96432 50281 53391
## HLA-B 97682 112829 112485 107813 83425 77180
## MICA 211 121 109 88 101 91
## LTA 62 38 42 38 49 35
## TNF 189 198 287 324 345 358
## HLA-DRB1 3522 3228 4888 3216 2731 3505
## HLA-DQB1 582 459 3847 496 496 594
## PPARD 345 231 263 232 274 245
## CCND3 3959 4472 3502 4961 5302 3453
## VEGFA 243 210 238 229 245 148
## RUNX2 507 462 539 453 785 497
## IL17A 0 0 1 0 0 0
## IL17F 0 0 0 0 0 0
## PRDM1 452 723 515 748 840 523
## ATG5 410 366 392 347 387 360
## TRAF3IP2 209 129 198 143 154 145
## NCOA7 255 449 337 259 280 216
## SGK1 1797 3312 3282 1862 2298 1597
## IFNGR1 2303 2674 2501 2458 3082 2243
## TNFAIP3 2968 3271 2108 7772 7770 5175
## SOD2 35021 44744 33172 28542 32003 27013
## LPAL2 27 11 11 13 15 19
## PLG 1 0 0 1 0 2
## CCR6 79 38 90 30 105 95
## RAC1 2683 3380 2915 2769 2863 2318
## ZNF316 1011 798 727 960 984 890
## AHR 672 854 838 1424 1223 655
## IL6 5 1 1 9 5 2
## TOMM7 2682 1692 2015 2251 2158 2208
## CYCS 516 545 605 546 456 505
## AQP1 6 2 2 2 4 2
## NT5C3A 748 785 655 513 605 473
## EGFR 0 0 0 0 0 0
## CD36 1880 2292 1957 2704 2250 902
## SAMD9 1344 1658 1529 645 568 560
## SERPINE1 6 13 5 8 8 8
## CUX1 1271 1374 1481 1504 1655 1115
## PSMC2 354 331 348 390 332 300
## NAMPT 41624 50520 37491 45618 54141 32282
## HYAL4 0 0 0 0 1 0
## LEP 7 0 10 1 0 2
## CALD1 26 14 13 8 28 16
## BRAF 654 538 610 598 629 398
## EZH2 66 42 84 51 45 58
## DNAJB6 1418 1702 1650 1634 1948 1200
## CSMD1 34 3 0 1 2 6
## CTSB 4263 6730 6198 4995 6425 4389
## EGR3 210 640 2164 143 213 206
## TNFRSF10A 207 91 134 136 100 112
## BNIP3L 2115 2320 2466 2003 2413 1725
## DUSP4 48 32 39 112 58 55
## NRG1 34 114 52 70 83 146
## RPL7 11502 8154 9142 8933 9979 8202
## IL7 17 20 13 4 4 9
## GEM 0 1 0 0 1 2
## MYC 598 666 549 396 320 199
## GPT 1 2 3 2 4 3
## JAK2 821 807 834 869 748 649
## CD274 102 181 102 73 54 57
## IL33 0 0 0 0 0 0
## LURAP1L-AS1 0 0 0 0 0 0
## LURAP1L 1 5 0 2 4 1
## TTC39B 215 100 129 128 127 105
## IFNA1 0 0 0 0 0 0
## TEK 21 20 17 7 18 23
## TRBV20OR9-2 0 0 0 0 0 0
## TOMM5 189 191 203 216 194 215
## ANXA1 6388 8511 5529 6977 6482 5730
## ERP44 1472 1403 1418 1272 1207 997
## ZNF483 42 28 28 38 31 28
## TNFSF15 8 2 12 0 0 4
## TLR4 3353 4013 4559 2093 2161 2441
## PTGS1 1372 847 560 691 1501 638
## HSPA5 5489 5258 6857 5022 4940 5444
## FNBP1 3626 3519 3592 2711 2980 2742
## CARD9 215 173 255 157 181 190
## TRAF2 134 94 126 110 111 99
## CLIC3 255 74 106 94 124 132
## IL2RA 125 47 79 81 45 69
## GATA3 439 271 297 249 346 253
## VIM 17449 21735 16181 14920 17459 15025
## CREM 193 149 163 192 202 182
## DKK1 0 0 0 0 0 0
## MBL2 0 0 0 0 0 0
## SAR1A 873 808 810 954 1130 797
## PRF1 3276 2027 2499 1731 1161 2970
## ZMIZ1 1901 2280 1811 2061 2489 1835
## IFIT3 2535 6148 2276 2907 1254 655
## TALDO1 8838 11437 10159 6978 8671 6566
## IGF2 0 0 0 0 0 0
## INS-IGF2 0 0 0 0 0 0
## IGF2-AS 0 0 0 0 0 0
## INS 0 0 0 0 0 0
## STIM1 1378 1088 1366 1077 1142 1117
## TRIM22 1822 2747 1852 1845 1292 1206
## PTH 0 0 0 0 0 0
## SAA1 0 0 0 0 0 0
## SLC1A2 3 0 2 1 1 3
## FOSL1 17 173 100 113 54 52
## CCND1 5 4 5 2 5 5
## JRKL 105 61 91 35 38 40
## MMP7 0 0 0 0 0 0
## MMP1 5 0 0 1 4 1
## MMP3 0 0 0 0 0 0
## CASP1 2618 3113 2870 2226 1927 2079
## DLAT 207 164 184 136 106 130
## IL18 118 94 101 168 108 104
## CD3E 3628 2810 2315 2201 2748 2565
## MCAM 222 194 239 229 242 167
## WNK1 3102 3598 4043 2371 2545 2205
## TNFRSF1A 2921 3766 2927 1481 1767 1763
## GAPDH 18555 21105 20679 18573 18995 16457
## CD4 4455 3739 3823 3737 3400 3043
## SLC2A3 4323 9149 11461 7363 8193 8858
## CLEC4D 241 481 273 408 215 250
## KLRB1 1110 499 963 837 936 684
## CD69 1467 1681 1284 2356 2239 1797
## CLEC2B 1882 2374 1929 1567 1715 1025
## OLR1 9 41 7 5 11 1
## ABCD2 176 105 102 83 96 89
## LRRK2 8254 8085 9732 5427 7310 4903
## VDR 380 476 417 271 370 221
## TMBIM6 12521 13597 14128 9071 10697 9857
## PFDN5 3783 3320 3207 3614 3429 3063
## SP7 0 0 0 0 0 0
## MUCL1 1 0 0 0 0 0
## CD63 2586 3887 2781 3677 3805 2687
## SUOX 1044 1078 1213 731 854 765
## RPS26 7342 3166 3207 854 804 699
## RPL41 8866 6705 6932 7573 7217 7622
## IL23A 39 25 42 24 25 24
## DDIT3 827 1056 747 901 1153 643
## IFNG 32 41 24 21 34 37
## IL22 0 0 1 0 1 1
## LYZ 82127 85154 42990 123617 96761 84499
## CAPS2 6 3 6 6 7 5
## SYT1 4 2 7 0 3 4
## BTG1 9977 11289 10127 12981 14883 8918
## HCAR3 1350 1805 2117 1041 1359 1259
## GJB2 0 1 8 0 2 1
## GJB6 16 39 48 51 31 36
## TNFSF11 2 1 1 5 0 0
## TPT1 65408 47294 47666 53395 73565 47265
## LMO7 75 55 60 37 49 40
## TNFSF13B 1811 2164 1639 1475 1242 1083
## LAMP1 2751 2923 3127 2378 2585 2165
## PSME2 1477 1780 1327 1579 956 1055
## GZMB 962 731 711 835 515 1301
## RPL36AL 2564 2415 2077 2228 2125 2001
## PYGL 4161 5502 5108 3962 4334 3371
## HIF1A 2140 2306 1982 3903 3857 2776
## FOS 35343 18666 55848 34775 39344 34967
## JDP2 836 949 922 1151 1167 827
## NOXRED1 9 4 9 5 7 2
## SERPINA1 20513 25645 15552 22153 24374 19074
## CDC42BPB 254 142 203 197 203 252
## PLA2G4D 0 0 0 0 0 0
## TRIM69 22 8 16 10 13 14
## SLC51B 0 0 0 0 0 0
## SMAD3 684 512 471 627 673 499
## CYP1A1 1 0 0 0 0 0
## AKAP13 3540 3587 4341 3645 3603 3007
## MEFV 2539 3168 2484 1771 1881 1694
## SOCS1 55 97 55 109 76 64
## ATXN2L 2240 1718 1755 1513 1643 1560
## CD19 190 45 156 92 49 102
## ITGAL 5856 5573 4872 5138 4998 5365
## ITGAM 4574 5464 5263 4383 4060 4574
## ITGAX 6362 5751 5668 5385 7010 5109
## DNAJA2 642 670 670 687 806 502
## SIAH1 114 115 128 162 144 135
## ADCY7 2628 2034 2430 1825 1755 1865
## NOD2 1363 480 821 464 469 329
## CMTM2 1860 2452 3301 1714 2234 1720
## SF3B3 890 670 854 464 482 580
## PSMD7 747 708 746 905 898 638
## WWOX 59 32 41 43 54 38
## MAF 540 407 393 313 283 460
## SLC7A5 346 248 304 523 799 392
## CXCL16 1442 2415 2056 2301 2591 1993
## XAF1 957 1321 588 594 369 432
## CD68 4100 4766 4030 5438 4802 3217
## PER1 617 972 558 3251 3687 1198
## NOS2 1 0 0 0 2 2
## TRAF4 154 92 122 134 120 132
## CCL2 1 22 15 7 0 3
## CCL5 5166 5789 2498 3479 4137 5158
## CCL3 176 86 223 90 152 249
## CCR7 646 320 499 268 326 241
## STAT3 4375 5047 4504 3078 3670 2859
## SOST 0 0 0 0 0 0
## ITGA2B 1268 668 230 360 1132 430
## EFCAB13 31 23 18 26 19 17
## NPEPPS 974 1002 1153 682 707 583
## TBX21 577 477 433 298 340 592
## COL1A1 0 0 1 0 3 0
## MRPS23 169 174 200 125 140 120
## MIR21 4 9 4 9 11 4
## RPS6KB1 369 294 314 246 314 215
## ACE 49 46 40 28 50 30
## ERN1 1118 1070 1254 947 1437 962
## PRTN3 10 29 5 16 9 16
## PLIN5 83 112 123 100 87 134
## RETN 78 109 45 98 113 71
## CCL25 0 0 0 1 0 0
## ICAM1 1554 2427 1666 2440 1999 1840
## TYK2 2156 2023 2532 1346 1639 1734
## SMARCA4 809 625 720 560 675 567
## ACP5 314 200 278 191 393 162
## JUNB 43937 34632 46114 44625 54433 53440
## CYP4F22 21 53 103 26 79 18
## JAK3 2285 1766 1798 1751 1538 1687
## JUND 9184 7564 8097 9073 9258 9244
## CEBPA 1076 715 872 1393 1355 944
## CEBPG 286 258 302 376 398 285
## ACP7 1 3 0 0 0 0
## ZFP36 24555 23923 30893 28726 35749 36442
## TGFB1 6754 7221 5726 6570 7041 6071
## RPS19 12618 8475 9337 9935 10739 8922
## PSG2 0 0 0 0 0 0
## FUT2 3 3 2 1 3 3
## NKG7 4546 4406 2782 3983 3107 5457
## ZNF415 5 7 8 0 15 4
## LILRB2 4562 4872 4890 4501 3998 3756
## LILRA5 2950 3242 2048 3000 1503 2922
## KIR3DL1 89 37 115 86 163 2
## KIR3DL2 52 45 42 72 44 40
## SMOX 173 132 101 103 212 131
## BMP2 3 9 27 5 4 1
## GINS1 5 4 8 7 6 7
## PLCG1 1014 601 720 524 565 610
## YWHAB 5646 5706 6365 4769 5057 5366
## PI3 198 1310 462 692 484 433
## MMP9 2728 5279 3958 1506 2596 2547
## CD40 162 126 134 114 66 109
## PFDN4 43 40 41 53 43 62
## BMP7 0 0 0 0 0 0
## RPS21 5735 4032 4357 4640 4740 4489
## MX1 875 1967 449 1153 456 423
## PFKL 1368 897 1235 966 1089 958
## IL17RA 4904 6010 5857 4430 4797 3788
## UBE2L3 1008 1066 996 818 874 763
## TPST2 1356 1348 1262 1208 1115 1350
## XBP1 1372 875 1214 1146 1062 989
## UQCR10 591 542 610 540 446 506
## SEC14L2 43 30 18 29 38 20
## APOL6 1261 1764 1275 1113 811 875
## APOL1 736 1038 720 370 306 348
## TYMP 4119 6005 3664 3981 4012 2773
## BEND2 80 40 24 51 136 37
## PHEX 12 3 10 13 7 9
## TIMP1 1188 2346 1264 1596 1573 1126
## FOXP3 68 40 73 40 50 35
## MSN 24123 26117 23743 20648 23508 19058
## PGK1 7233 7822 7441 7460 7524 6392
## LAMP2 6286 7291 7121 4953 6002 4160
## CD40LG 174 134 180 111 151 102
## IRAK1 1779 1497 1806 1849 1726 1640
## COX2 58938 48093 52101 59809 57247 53089
## GSM3308437 GSM3308438 GSM3308439 GSM3308440 GSM3308441 GSM3308442
## TNFRSF9 56 281 141 175 132 185
## ENO1 4923 6091 5444 7114 7361 5566
## PIK3CD 2765 7917 7447 7727 7559 5956
## PGD 2629 8544 4894 7199 5436 3916
## MTHFR 365 328 422 277 691 351
## TNFRSF1B 7984 15137 12857 12853 15958 14463
## PINK1 268 1013 759 971 901 714
## IFNLR1 60 12 79 43 91 73
## RUNX3 5154 2250 3378 2209 5034 5005
## SH3BGRL3 6216 11108 9709 10201 12548 10289
## CD52 3729 2351 4022 4632 6073 5150
## IFI6 2099 1728 758 1357 750 915
## ZC3H12A 556 569 491 556 547 590
## UTP11 87 111 103 116 98 103
## JUN 5433 2527 3117 4387 23735 1084
## KANK4 5 0 0 0 0 0
## EFCAB7 23 25 42 20 28 29
## IL23R 3 0 6 3 3 5
## ADGRL2 14 0 0 0 0 1
## GBP3 187 313 283 117 314 192
## GBP1 1028 1570 960 808 620 394
## GBP5 2916 3154 3431 954 2042 1244
## TGFBR3 1425 403 679 352 1127 1074
## VCAM1 26 1 3 0 2 4
## PTPN22 312 382 508 379 426 485
## CD160 176 24 74 84 125 58
## FCGR1A 230 1224 456 754 383 331
## MCL1 17214 28958 25812 23374 24315 30010
## CTSK 61 61 80 56 85 74
## RORC 36 12 69 36 34 61
## S100A9 53018 183796 98212 204593 98291 104071
## S100A12 1397 5787 3124 7757 3299 2257
## S100A8 20928 66703 36312 81933 34596 38474
## IL6R 1297 5140 4595 4003 4668 3897
## RIT1 951 1604 1248 1493 1043 1242
## BGLAP 3 10 11 7 6 7
## IFI16 1904 3123 2627 3222 1829 2700
## AIM2 61 140 99 150 70 63
## CRP 3 0 0 0 0 0
## FCGR2A 4599 13139 11555 16028 10611 12181
## HSPA6 688 2340 2048 3189 1420 1320
## FCGR3A 14166 21212 15324 16735 14743 14035
## SELL 11914 42366 26385 34119 28601 26363
## GLUL 8440 16472 13074 16238 12875 17454
## PTGS2 1976 6281 7613 4968 12795 7467
## CRB1 10 0 0 1 1 3
## KDM5B 277 519 474 401 423 428
## IL10 8 6 0 3 1 5
## YOD1 353 358 456 260 183 291
## HHAT 39 27 41 23 36 36
## TRAF5 294 128 501 273 439 347
## NLRP3 876 903 579 859 964 865
## LINC01250 1 0 0 0 1 0
## RPS7 7039 5987 8152 8756 9627 10653
## RSAD2 2907 877 279 374 205 159
## FOSL2 4202 5056 3816 3766 3547 4681
## REL 1162 935 1293 746 1066 896
## TGFA 234 440 581 642 474 408
## DYSF 1686 7305 3990 5296 3568 3513
## HK2 514 1711 1079 938 1000 733
## CD8A 1751 1447 1860 888 2826 2779
## CD8B 688 356 477 522 1268 810
## EIF5B 396 334 601 392 532 447
## IL1R1 114 329 271 327 185 406
## RGPD6 75 51 103 58 77 77
## IL1A 4 0 0 2 1 0
## IL1B 266 425 321 1641 842 292
## IL37 5 0 0 0 0 0
## IL36RN 3 0 0 0 0 0
## IL1F10 2 0 0 0 0 0
## IL1RN 1444 2187 1882 4428 2034 2415
## NMI 904 2431 1341 2082 1054 1333
## TNFAIP6 220 429 466 503 219 827
## IFIH1 502 470 403 381 309 327
## SCN1A 23 0 0 0 0 0
## ABCB11 15 1 0 1 2 0
## RBM45 52 33 76 30 57 38
## FRZB 2 0 0 0 0 0
## TFPI 9 3 6 3 7 1
## STAT1 3224 5595 4138 3659 3019 2193
## NABP1 337 711 820 749 511 635
## SF3B1 4080 4841 5548 3984 4048 4936
## CASP10 333 338 382 259 464 356
## CD28 568 189 676 480 606 472
## CTLA4 120 49 106 79 30 116
## ICOS 138 51 216 159 165 178
## NDUFS1 393 499 545 389 509 515
## CXCR2 5731 18676 18566 19453 17748 22622
## IRS1 36 13 89 42 97 44
## CCL20 3 0 1 2 3 3
## ATG16L1 351 248 372 267 374 384
## GPR35 128 175 106 123 125 125
## PDCD1 30 24 29 22 46 31
## PPARG 11 14 3 4 14 2
## RPL15 9401 9530 12659 12474 16730 15250
## EOMES 207 80 109 62 302 181
## CX3CR1 658 868 955 1101 2019 689
## ACKR2 10 2 2 0 0 2
## CCR2 207 544 667 613 891 494
## CCRL2 37 31 30 23 30 19
## TLR9 32 63 100 75 73 45
## ARHGEF3 1062 788 1125 840 1206 992
## ADAMTS9 12 0 0 0 0 1
## TMEM45A 8 4 2 6 0 0
## CD80 4 5 9 2 4 9
## CD86 650 1218 713 634 1194 880
## MIX23 15 13 23 27 27 29
## PLS1 20 7 15 11 30 20
## PTX3 78 62 52 86 50 8
## GOLIM4 56 88 101 55 123 84
## MYNN 373 355 325 290 367 358
## TNFSF10 1525 3917 2870 3934 2549 2692
## ADIPOQ 5 0 0 0 0 0
## SPON2 805 145 462 287 628 582
## S100P 1524 3327 3162 2847 2810 1561
## WDR1 3728 6978 5863 6522 5985 5370
## CD38 397 174 374 178 279 139
## PPARGC1A 22 2 1 2 6 10
## TMPRSS11B 3 0 0 0 0 0
## CSN3 0 0 0 0 0 0
## ALB 3 0 1 0 0 1
## CXCL8 11591 14955 22229 16980 47195 12713
## CXCL2 17 18 3 6 33 4
## AREG 195 93 27 22 20 140
## CXCL10 41 23 16 21 21 1
## CXCL13 1 2 0 0 0 1
## SPP1 17 62 113 26 48 90
## HERC6 287 164 177 256 167 178
## NFKB1 719 729 944 1007 807 910
## SEC24B 359 515 531 415 447 555
## EGF 24 29 25 18 20 12
## IL2 4 0 2 2 0 5
## IL21 2 0 0 0 0 2
## IL21-AS1 6 1 3 1 0 0
## SLC7A11 13 10 13 8 10 10
## IL15 56 91 63 49 104 99
## EDNRA 7 0 0 0 0 0
## TLR2 2041 3478 3514 2879 2498 3750
## FGB 5 0 0 0 0 0
## DDX60 791 382 324 297 285 260
## SPCS3 1330 1864 1949 1812 1781 2041
## TLR3 15 5 12 3 18 19
## OSMR 32 28 49 22 19 26
## GZMK 768 326 753 354 1138 533
## GZMA 1640 751 1005 581 2192 1223
## ANKRD55 29 81 122 106 65 23
## CENPK 80 11 140 110 53 124
## CAST 2042 4155 3152 2502 3496 2832
## ERAP1 1228 1849 1580 924 1973 1222
## ERAP2 1420 171 1598 146 1668 201
## TNFAIP8 859 1010 1647 1257 1271 1288
## CSF2 0 0 0 2 0 2
## IL5 3 0 3 0 1 0
## IL13 3 0 0 0 0 0
## IL4 2 4 8 4 9 1
## CD14 3334 7188 5266 8222 9686 7144
## CSNK1A1 931 1817 1733 1564 1593 1565
## PPARGC1B 165 156 133 82 178 71
## TNIP1 2857 5286 4404 6048 4412 4070
## ATOX1 105 206 154 161 209 184
## FAXDC2 134 133 178 111 192 110
## IL12B 7 0 0 0 0 0
## MIR146A 0 0 0 0 0 0
## PDLIM7 577 2596 1675 2156 1736 1648
## SERPINB1 2559 4934 3706 6307 4010 4906
## SSR1 1493 2446 2422 2132 2382 2190
## CD83 491 271 272 221 611 374
## SOX4 124 249 232 147 157 120
## CMAHP 103 45 104 65 102 81
## HLA-A 33819 58020 38549 37633 40095 36373
## HLA-C 47620 126512 95391 81409 59363 88108
## HLA-B 69256 132999 124957 93415 94895 99189
## MICA 106 88 164 130 264 137
## LTA 43 25 63 57 73 35
## TNF 252 254 198 168 194 99
## HLA-DRB1 5050 5653 6527 3718 6850 3349
## HLA-DQB1 3747 4545 3323 659 950 903
## PPARD 195 243 415 285 370 359
## CCND3 3439 5244 3514 4179 4547 5360
## VEGFA 177 277 166 222 198 303
## RUNX2 428 440 623 451 348 879
## IL17A 2 0 0 0 0 0
## IL17F 3 0 0 0 0 0
## PRDM1 746 412 688 510 411 1248
## ATG5 361 399 441 389 347 454
## TRAF3IP2 130 116 185 186 178 226
## NCOA7 381 301 304 304 376 337
## SGK1 1706 2080 2256 2635 4011 1276
## IFNGR1 1433 3404 3130 3571 2529 3241
## TNFAIP3 6091 2606 2709 2330 4316 5724
## SOD2 12639 43231 35934 42482 27510 42433
## LPAL2 27 7 22 15 35 18
## PLG 13 0 0 0 0 0
## CCR6 87 16 105 72 57 117
## RAC1 1568 3154 2868 2921 2737 3379
## ZNF316 334 862 831 866 696 766
## AHR 935 666 865 566 1237 794
## IL6 10 1 4 3 5 2
## TOMM7 1693 1650 2279 1964 2184 2485
## CYCS 667 419 558 522 686 529
## AQP1 1 3 1 3 2 0
## NT5C3A 511 981 778 942 692 734
## EGFR 24 0 0 0 0 0
## CD36 2207 2776 2343 2185 2593 1356
## SAMD9 1333 1551 1600 1363 1511 1307
## SERPINE1 7 10 17 2 21 5
## CUX1 999 1939 1536 1179 1936 1145
## PSMC2 356 310 366 316 384 374
## NAMPT 21743 47631 38500 62539 28326 55021
## HYAL4 5 0 0 0 0 0
## LEP 4 1 6 0 4 2
## CALD1 17 10 28 2 5 2
## BRAF 440 790 800 638 643 771
## EZH2 78 36 91 50 74 65
## DNAJB6 995 1628 1678 2000 1346 1574
## CSMD1 38 0 1 3 0 2
## CTSB 5693 5838 4541 5600 6759 5872
## EGR3 224 162 150 204 662 180
## TNFRSF10A 121 97 239 165 149 127
## BNIP3L 1170 3122 2093 2299 2007 2164
## DUSP4 137 26 57 64 42 157
## NRG1 49 127 49 218 154 136
## RPL7 6387 6080 9748 8789 10058 11335
## IL7 14 13 31 8 11 25
## GEM 4 0 3 1 2 0
## MYC 204 266 602 960 365 577
## GPT 6 2 4 1 3 1
## JAK2 668 1677 980 965 1115 640
## CD274 94 113 178 160 64 98
## IL33 13 0 0 0 0 0
## LURAP1L-AS1 0 0 0 0 0 0
## LURAP1L 4 1 6 1 3 0
## TTC39B 145 116 250 97 202 130
## IFNA1 2 0 0 0 0 0
## TEK 17 15 62 43 5 8
## TRBV20OR9-2 0 0 0 0 0 0
## TOMM5 178 163 188 185 221 243
## ANXA1 5799 5779 5582 6371 7686 10395
## ERP44 928 1661 1320 1361 1437 1242
## ZNF483 47 18 48 25 29 21
## TNFSF15 8 13 9 10 9 1
## TLR4 1665 6188 2443 4343 5121 5763
## PTGS1 379 711 717 480 963 452
## HSPA5 4284 4856 5128 6280 5741 5137
## FNBP1 2316 3467 4011 3533 3720 3699
## CARD9 94 212 175 139 285 130
## TRAF2 96 88 160 96 155 95
## CLIC3 92 30 95 62 175 105
## IL2RA 108 51 132 148 91 151
## GATA3 321 131 341 397 480 539
## VIM 10419 18909 12897 22381 19048 18529
## CREM 273 115 177 163 107 283
## DKK1 3 0 0 0 0 0
## MBL2 5 0 0 0 0 0
## SAR1A 777 885 851 755 704 781
## PRF1 3841 1297 2500 1119 2469 2534
## ZMIZ1 1235 2269 2246 1352 3028 2243
## IFIT3 7701 5132 2881 3749 1624 1756
## TALDO1 3265 11814 8570 11474 8760 8569
## IGF2 3 0 0 0 0 0
## INS-IGF2 3 0 0 0 0 0
## IGF2-AS 2 0 0 0 0 0
## INS 0 0 0 0 0 0
## STIM1 1061 1252 1348 1189 1518 1168
## TRIM22 2880 3186 2156 2030 1611 1661
## PTH 1 0 0 0 0 0
## SAA1 2 0 1 0 0 0
## SLC1A2 24 1 1 0 5 0
## FOSL1 76 51 15 52 28 36
## CCND1 8 5 5 4 6 3
## JRKL 45 60 98 38 93 71
## MMP7 2 0 0 0 0 0
## MMP1 3 1 2 2 0 1
## MMP3 3 0 0 0 0 0
## CASP1 1862 3951 2535 2944 2577 2895
## DLAT 168 154 192 161 249 198
## IL18 63 139 102 113 130 81
## CD3E 2509 1579 3422 2759 4050 3680
## MCAM 165 310 299 253 246 210
## WNK1 2139 3490 4348 2557 4519 3637
## TNFRSF1A 1011 3338 3705 3727 4082 2918
## GAPDH 13322 20989 13791 20838 19931 17347
## CD4 2884 3784 3678 4169 4934 3240
## SLC2A3 3476 10019 8524 13580 7168 9516
## CLEC4D 321 1079 185 878 356 355
## KLRB1 883 197 708 635 799 780
## CD69 2693 826 1260 1618 2043 2040
## CLEC2B 1157 2059 1329 2404 1346 1538
## OLR1 11 11 16 66 2 9
## ABCD2 132 64 238 113 175 126
## LRRK2 3707 11541 8528 7689 6570 7067
## VDR 285 454 404 476 467 326
## TMBIM6 6876 14303 13117 12811 14589 13198
## PFDN5 2744 3150 3155 3164 3448 4017
## SP7 2 0 0 0 0 0
## MUCL1 1 0 0 0 0 0
## CD63 2127 4186 2453 3606 3109 3573
## SUOX 568 1193 1131 1182 1138 1145
## RPS26 2718 705 694 3135 4185 815
## RPL41 5851 5036 6872 7389 8218 8781
## IL23A 22 15 33 23 29 32
## DDIT3 506 957 620 846 615 746
## IFNG 68 19 31 27 106 7
## IL22 2 2 0 1 0 1
## LYZ 53655 87349 35621 116350 47676 118507
## CAPS2 15 3 3 5 5 2
## SYT1 4 3 3 1 11 3
## BTG1 8905 12080 9496 10602 9468 12552
## HCAR3 528 1070 1476 3320 1580 1051
## GJB2 2 9 0 3 1 1
## GJB6 9 92 22 32 13 19
## TNFSF11 3 0 0 3 3 2
## TPT1 32490 41368 50160 60578 57563 63436
## LMO7 53 30 98 55 69 41
## TNFSF13B 1518 2285 1895 2667 1674 2967
## LAMP1 1826 2922 2692 2545 3116 2697
## PSME2 1451 1820 1355 1222 1422 876
## GZMB 2078 609 822 482 1122 1904
## RPL36AL 1591 2034 2356 2274 2466 2583
## PYGL 1307 7971 3794 7545 4023 4650
## HIF1A 2187 2543 2039 2179 1589 2254
## FOS 15403 47157 25985 34691 74159 12952
## JDP2 491 1215 834 980 822 1180
## NOXRED1 9 11 10 7 7 7
## SERPINA1 13309 26390 25903 26305 19232 22240
## CDC42BPB 146 182 265 159 343 197
## PLA2G4D 9 0 0 0 0 0
## TRIM69 23 10 16 15 10 15
## SLC51B 2 0 0 0 0 0
## SMAD3 622 416 621 483 767 578
## CYP1A1 5 2 1 3 1 1
## AKAP13 3317 4293 3972 2830 4103 4032
## MEFV 1108 3706 2922 3060 2909 3062
## SOCS1 23 46 57 73 87 58
## ATXN2L 1170 1565 2000 1556 2372 1802
## CD19 67 20 192 112 134 161
## ITGAL 5764 6014 5561 4413 7071 4926
## ITGAM 2826 6723 4613 5423 6130 5116
## ITGAX 2514 6980 5970 6526 5411 5930
## DNAJA2 464 810 689 668 672 790
## SIAH1 127 132 172 97 96 133
## ADCY7 1802 2643 2684 1777 3628 2656
## NOD2 434 1234 826 926 518 440
## CMTM2 708 2984 2385 3240 1504 1781
## SF3B3 637 616 904 734 1093 700
## PSMD7 720 789 651 702 694 760
## WWOX 43 33 48 47 56 39
## MAF 441 272 607 372 532 480
## SLC7A5 372 173 219 135 235 381
## CXCL16 1067 2640 1318 2053 1885 3313
## XAF1 1867 1409 968 671 685 677
## CD68 3840 5446 3561 3785 4926 3754
## PER1 1312 1104 656 351 637 1727
## NOS2 11 1 1 0 3 0
## TRAF4 108 47 134 73 134 103
## CCL2 16 1 4 6 19 5
## CCL5 6625 2716 3542 2073 6779 5328
## CCL3 341 157 92 95 391 49
## CCR7 193 152 987 493 655 343
## STAT3 2263 5627 4979 4801 3743 4747
## SOST 2 0 0 0 0 0
## ITGA2B 236 400 510 271 383 128
## EFCAB13 26 12 41 15 12 26
## NPEPPS 477 1210 966 1007 899 945
## TBX21 578 201 446 204 591 568
## COL1A1 12 3 2 1 0 0
## MRPS23 149 151 188 185 147 190
## MIR21 2 11 6 4 3 5
## RPS6KB1 275 267 434 345 396 409
## ACE 49 18 45 41 62 66
## ERN1 737 1095 1273 840 1388 1990
## PRTN3 9 21 3 27 7 10
## PLIN5 51 125 108 180 80 124
## RETN 37 109 49 162 101 83
## CCL25 3 2 1 0 1 0
## ICAM1 1264 1818 1194 1590 1375 1170
## TYK2 987 2387 2261 1791 2110 1952
## SMARCA4 473 574 814 596 912 665
## ACP5 222 307 354 312 579 221
## JUNB 11973 36103 27082 69331 27132 16330
## CYP4F22 16 28 28 46 37 6
## JAK3 1191 1693 2282 2079 1545 1871
## JUND 3004 4575 4827 6333 13900 5709
## CEBPA 559 1494 1034 1171 981 631
## CEBPG 287 293 276 286 292 302
## ACP7 10 0 0 2 2 0
## ZFP36 13394 26302 15591 48473 25928 8984
## TGFB1 2695 5935 4784 5824 6167 4534
## RPS19 7440 5985 9508 9684 11406 11133
## PSG2 4 0 0 0 0 0
## FUT2 7 0 4 1 3 1
## NKG7 6802 2507 3034 2375 6380 5434
## ZNF415 11 6 8 16 15 7
## LILRB2 3453 6582 4908 4898 4897 4438
## LILRA5 2001 5400 2844 4145 2932 2661
## KIR3DL1 146 11 55 23 91 289
## KIR3DL2 145 18 26 41 28 66
## SMOX 72 85 118 70 150 65
## BMP2 3 8 4 12 4 12
## GINS1 15 4 9 8 7 10
## PLCG1 663 335 1068 582 988 661
## YWHAB 4054 7361 5755 6023 6069 5103
## PI3 147 1768 683 1504 951 444
## MMP9 240 8338 1685 4703 2338 1219
## CD40 141 71 203 147 145 112
## PFDN4 61 31 52 43 34 55
## BMP7 5 0 0 0 0 0
## RPS21 3131 2803 4609 4485 4947 5372
## MX1 1728 1546 965 1329 732 1259
## PFKL 658 1025 1167 1011 1526 1194
## IL17RA 1853 7514 5531 5383 5338 4896
## UBE2L3 756 1104 1022 1004 1156 1054
## TPST2 1018 1104 1314 1104 1787 1264
## XBP1 976 794 1137 1080 1005 1239
## UQCR10 380 608 562 536 636 568
## SEC14L2 18 19 46 30 42 21
## APOL6 1709 1498 1716 942 1123 832
## APOL1 404 834 757 502 622 406
## TYMP 2356 4757 3385 4088 3641 2554
## BEND2 28 58 51 26 51 19
## PHEX 29 4 29 4 11 16
## TIMP1 1147 2180 1041 1505 1924 2198
## FOXP3 77 32 87 54 95 92
## MSN 15577 28501 23537 22925 28237 22201
## PGK1 5391 8888 7006 9001 7795 7335
## LAMP2 2846 8642 7117 7069 5850 6385
## CD40LG 102 59 207 166 169 192
## IRAK1 1039 1574 1642 1507 1961 1704
## COX2 40808 32486 43141 47537 68415 48921
## GSM3308443 GSM3308444 GSM3308445 GSM3308446 GSM3308447 GSM3308448
## TNFRSF9 89 110 76 205 155 18
## ENO1 6388 5838 7148 6613 6882 2125
## PIK3CD 6047 6453 6022 6198 6502 2641
## PGD 4299 4762 5385 5830 4844 1687
## MTHFR 404 451 455 280 395 129
## TNFRSF1B 13726 13272 13292 15217 16715 4731
## PINK1 675 654 695 858 695 237
## IFNLR1 67 46 34 60 58 11
## RUNX3 5689 3061 4882 4369 4341 941
## SH3BGRL3 9597 9560 13230 13773 13168 4361
## CD52 4748 3841 3960 5492 4979 2274
## IFI6 597 1835 1271 1468 1035 227
## ZC3H12A 563 457 855 739 790 146
## UTP11 113 95 113 103 114 17
## JUN 1578 7170 6433 8679 9152 1798
## KANK4 1 0 0 0 0 0
## EFCAB7 21 28 28 17 31 7
## IL23R 0 2 0 1 7 1
## ADGRL2 0 0 0 0 0 0
## GBP3 220 207 195 203 192 63
## GBP1 449 597 436 589 490 106
## GBP5 2150 2352 1478 1611 2140 216
## TGFBR3 1034 520 703 904 862 123
## VCAM1 1 5 4 4 1 0
## PTPN22 385 388 343 361 345 79
## CD160 142 88 232 121 132 26
## FCGR1A 349 430 399 453 475 79
## MCL1 24519 21995 24552 21580 24402 3764
## CTSK 72 80 80 61 45 18
## RORC 34 37 25 26 57 30
## S100A9 75498 113153 116100 143716 139545 38998
## S100A12 2815 4254 3124 4969 3730 934
## S100A8 25950 42740 39429 54411 54618 20094
## IL6R 3201 3642 2723 3481 3372 1423
## RIT1 1316 1437 1589 1303 1476 251
## BGLAP 5 5 10 9 8 7
## IFI16 1572 2681 1528 2212 2150 394
## AIM2 29 72 46 86 97 25
## CRP 0 0 0 0 0 1
## FCGR2A 7483 11092 9501 10336 12320 1952
## HSPA6 1199 1251 1188 1928 1662 559
## FCGR3A 11591 8457 12475 14033 15829 2435
## SELL 22826 31752 27342 40278 29349 6076
## GLUL 12012 17941 15873 17482 17637 3610
## PTGS2 806 5585 3574 6828 3796 167
## CRB1 1 0 1 0 2 0
## KDM5B 454 409 457 364 392 105
## IL10 7 3 0 10 5 0
## YOD1 531 319 423 220 333 41
## HHAT 62 35 28 25 57 7
## TRAF5 401 341 260 175 339 165
## NLRP3 935 829 1299 719 834 162
## LINC01250 0 0 0 0 0 0
## RPS7 9616 6607 10835 8237 10543 3786
## RSAD2 118 973 219 392 253 32
## FOSL2 5016 4446 6078 4644 4938 487
## REL 1310 1158 1124 627 858 175
## TGFA 391 447 530 419 544 54
## DYSF 2500 3776 2502 3792 3652 951
## HK2 890 967 936 1089 729 166
## CD8A 2145 1554 1180 2761 2390 642
## CD8B 916 839 510 1227 1024 533
## EIF5B 545 421 428 424 432 617
## IL1R1 216 248 245 222 329 48
## RGPD6 110 60 70 46 74 42
## IL1A 1 0 0 0 0 0
## IL1B 55 289 412 330 369 47
## IL37 1 1 0 0 0 0
## IL36RN 0 0 0 0 0 0
## IL1F10 0 0 0 0 0 0
## IL1RN 979 2156 2141 2976 2632 1011
## NMI 889 1350 1003 1583 1312 230
## TNFAIP6 185 397 220 505 559 109
## IFIH1 325 375 308 320 331 48
## SCN1A 0 0 0 0 0 0
## ABCB11 0 0 0 0 0 0
## RBM45 45 56 48 44 49 10
## FRZB 0 0 0 0 0 0
## TFPI 3 1 2 4 3 6
## STAT1 3437 3525 3055 3105 3363 600
## NABP1 382 683 417 487 594 96
## SF3B1 4482 4658 4649 3695 4428 905
## CASP10 384 314 324 262 277 109
## CD28 1169 618 716 351 613 263
## CTLA4 197 80 98 84 80 32
## ICOS 246 121 168 88 149 55
## NDUFS1 557 461 493 470 490 127
## CXCR2 11280 17627 11707 16244 16173 2143
## IRS1 44 67 40 19 33 29
## CCL20 0 1 0 3 5 0
## ATG16L1 549 348 413 350 384 132
## GPR35 203 142 168 152 154 70
## PDCD1 70 29 33 65 21 6
## PPARG 4 1 4 5 3 0
## RPL15 15247 12037 17297 12327 15527 5675
## EOMES 215 94 89 226 111 33
## CX3CR1 410 684 302 732 457 125
## ACKR2 0 0 2 0 3 2
## CCR2 415 312 387 439 235 148
## CCRL2 35 38 43 41 35 9
## TLR9 50 77 57 49 61 31
## ARHGEF3 1441 1090 1140 1127 1136 283
## ADAMTS9 0 0 0 0 0 0
## TMEM45A 1 2 1 2 3 4
## CD80 8 7 6 1 6 0
## CD86 823 852 1014 887 861 214
## MIX23 25 23 24 16 16 17
## PLS1 25 17 18 10 21 6
## PTX3 28 58 99 41 38 9
## GOLIM4 92 64 105 72 59 22
## MYNN 353 275 406 320 402 66
## TNFSF10 1639 2277 1403 2195 1944 328
## ADIPOQ 0 0 0 0 0 0
## SPON2 520 574 989 842 552 49
## S100P 131 3625 4006 5603 4442 161
## WDR1 5355 5049 5425 6046 5419 1630
## CD38 240 292 277 149 209 38
## PPARGC1A 6 14 5 3 8 1
## TMPRSS11B 0 0 0 0 0 0
## CSN3 0 0 0 0 0 0
## ALB 0 1 0 0 0 0
## CXCL8 4876 41735 64868 43159 27905 2948
## CXCL2 1 5 21 8 11 0
## AREG 284 26 90 72 67 4
## CXCL10 9 14 17 20 15 1
## CXCL13 0 0 0 2 0 0
## SPP1 57 145 54 17 4 3
## HERC6 148 238 259 160 190 72
## NFKB1 1155 828 897 746 809 286
## SEC24B 654 473 513 372 407 158
## EGF 30 19 29 19 25 9
## IL2 3 0 3 2 0 0
## IL21 0 0 0 0 1 0
## IL21-AS1 0 1 1 0 0 0
## SLC7A11 6 9 12 7 6 2
## IL15 56 59 63 76 74 26
## EDNRA 0 0 0 0 0 0
## TLR2 2963 2301 2131 2835 2327 438
## FGB 0 0 0 0 0 0
## DDX60 261 395 253 345 241 63
## SPCS3 2078 1511 1592 1931 1997 468
## TLR3 7 11 5 8 12 0
## OSMR 35 30 31 19 20 2
## GZMK 1290 747 557 913 749 166
## GZMA 1160 690 1230 2045 1213 197
## ANKRD55 111 37 102 41 62 48
## CENPK 122 98 21 39 69 5
## CAST 2755 3039 3101 2805 2307 585
## ERAP1 1453 1577 1879 1123 1117 260
## ERAP2 1883 1186 1392 1040 2530 1083
## TNFAIP8 1441 1226 1113 952 1185 511
## CSF2 0 0 0 0 0 0
## IL5 0 0 0 0 0 0
## IL13 1 0 1 0 0 1
## IL4 2 1 6 0 7 4
## CD14 6376 5947 8166 9455 8430 3254
## CSNK1A1 1424 1379 1349 1585 1382 574
## PPARGC1B 159 99 131 92 111 18
## TNIP1 3916 4515 4453 4794 5219 1552
## ATOX1 187 154 179 247 165 131
## FAXDC2 183 155 175 159 133 85
## IL12B 1 0 0 0 0 0
## MIR146A 0 0 0 0 0 0
## PDLIM7 1246 1770 1613 2194 2068 599
## SERPINB1 2911 4643 3867 4331 5136 1406
## SSR1 2349 2213 2261 2167 2332 450
## CD83 331 316 637 349 404 143
## SOX4 196 291 338 249 206 179
## CMAHP 100 65 70 63 86 38
## HLA-A 50273 35150 50187 53123 55509 18332
## HLA-C 82242 86630 77811 73045 76808 15075
## HLA-B 102024 85207 110902 109018 100757 27745
## MICA 104 134 143 113 132 68
## LTA 49 57 51 35 50 32
## TNF 149 229 278 221 228 118
## HLA-DRB1 8402 3579 5568 6344 5188 957
## HLA-DQB1 3816 269 1714 1480 416 199
## PPARD 486 335 402 254 322 169
## CCND3 6591 3483 4060 4398 4106 1358
## VEGFA 188 193 279 205 214 12
## RUNX2 635 543 630 505 526 99
## IL17A 0 0 0 0 0 0
## IL17F 0 0 1 0 0 0
## PRDM1 1435 391 521 632 508 111
## ATG5 555 396 468 455 473 138
## TRAF3IP2 218 219 181 111 198 59
## NCOA7 364 271 302 217 311 119
## SGK1 995 1779 4580 1423 1921 254
## IFNGR1 3120 2704 2471 2932 2587 513
## TNFAIP3 9198 2576 5582 4987 4762 439
## SOD2 25772 37038 37619 41494 41172 7874
## LPAL2 17 11 16 15 18 2
## PLG 0 1 1 0 0 0
## CCR6 159 72 47 67 72 31
## RAC1 2920 2266 3050 3881 3252 1498
## ZNF316 811 819 838 614 1025 478
## AHR 1188 784 1299 841 749 197
## IL6 2 1 2 1 6 1
## TOMM7 2613 2028 1973 1572 2790 1222
## CYCS 601 487 560 599 595 133
## AQP1 5 1 2 5 5 0
## NT5C3A 633 602 567 785 621 313
## EGFR 0 0 0 0 0 0
## CD36 2002 1826 2873 2567 2009 452
## SAMD9 875 1368 770 1124 976 166
## SERPINE1 4 8 12 12 2 3
## CUX1 1357 1446 1700 1332 1563 397
## PSMC2 431 322 378 384 342 89
## NAMPT 33090 44660 43585 52984 49331 5815
## HYAL4 0 0 1 1 0 0
## LEP 0 4 0 3 3 0
## CALD1 13 19 7 19 14 3
## BRAF 637 654 588 534 579 143
## EZH2 69 45 62 50 68 29
## DNAJB6 1828 1423 1861 1575 1689 518
## CSMD1 2 4 2 0 2 8
## CTSB 6465 5365 5988 5741 5745 1371
## EGR3 28 209 124 311 226 37
## TNFRSF10A 245 220 167 109 126 50
## BNIP3L 2086 1942 2300 2448 2157 461
## DUSP4 276 91 158 79 76 17
## NRG1 30 35 240 27 73 12
## RPL7 11952 9631 12324 8618 11556 6141
## IL7 8 11 11 10 11 8
## GEM 3 0 2 0 3 0
## MYC 583 417 473 190 510 354
## GPT 0 1 1 3 7 1
## JAK2 879 833 808 685 831 183
## CD274 82 98 73 75 106 12
## IL33 0 0 0 0 0 1
## LURAP1L-AS1 0 0 0 0 0 0
## LURAP1L 0 1 2 2 1 2
## TTC39B 289 195 172 113 160 94
## IFNA1 0 0 0 0 0 0
## TEK 5 4 46 40 3 15
## TRBV20OR9-2 0 0 0 0 0 0
## TOMM5 209 177 247 235 242 78
## ANXA1 6777 5312 8239 7822 6583 1291
## ERP44 1231 1170 1330 1480 1462 335
## ZNF483 45 52 37 23 38 10
## TNFSF15 1 7 6 2 4 3
## TLR4 2166 3647 1929 4367 3301 761
## PTGS1 909 751 989 643 729 230
## HSPA5 5643 4532 6215 7099 6047 1165
## FNBP1 3451 3632 3393 3292 3550 962
## CARD9 176 168 177 221 185 65
## TRAF2 152 114 150 120 120 83
## CLIC3 110 139 156 128 148 49
## IL2RA 129 105 132 60 93 46
## GATA3 496 303 461 209 513 167
## VIM 15064 15559 17316 20522 19225 4926
## CREM 312 183 284 221 207 52
## DKK1 0 0 0 0 0 0
## MBL2 0 0 0 0 0 0
## SAR1A 1189 776 1138 948 953 319
## PRF1 2706 1925 2566 3477 2339 302
## ZMIZ1 2400 1988 2493 2038 2354 273
## IFIT3 1112 4452 2021 3746 1910 292
## TALDO1 6766 8364 9312 10485 9895 3119
## IGF2 0 0 0 0 0 1
## INS-IGF2 0 0 0 0 0 1
## IGF2-AS 0 0 0 0 0 0
## INS 0 0 0 0 0 0
## STIM1 1488 1158 1309 1203 1290 351
## TRIM22 1597 2273 1759 1973 1606 407
## PTH 0 0 0 0 0 0
## SAA1 0 0 1 0 0 0
## SLC1A2 2 1 4 4 4 0
## FOSL1 8 32 77 36 53 2
## CCND1 6 5 5 9 7 2
## JRKL 66 83 43 46 44 22
## MMP7 0 0 0 0 0 0
## MMP1 1 0 1 0 0 0
## MMP3 0 0 0 0 0 0
## CASP1 2282 2209 2553 2736 2567 649
## DLAT 171 156 183 164 173 40
## IL18 102 91 100 110 111 20
## CD3E 3950 2603 3011 3225 3791 1400
## MCAM 274 226 249 349 221 73
## WNK1 3623 3431 2670 2854 2648 509
## TNFRSF1A 1937 2912 2378 2887 2752 929
## GAPDH 16511 16308 18451 20742 18011 6618
## CD4 4970 4194 5187 4206 3946 939
## SLC2A3 6879 8989 11735 11064 10840 1605
## CLEC4D 282 321 171 384 278 88
## KLRB1 579 754 793 829 1482 244
## CD69 2205 1332 2166 2214 2198 152
## CLEC2B 1154 1388 1754 2141 1843 561
## OLR1 4 3 7 12 4 0
## ABCD2 198 141 163 98 159 91
## LRRK2 5250 7250 5160 6591 5152 679
## VDR 298 438 192 337 347 85
## TMBIM6 10987 11146 11896 12720 12535 2707
## PFDN5 3457 2993 4540 3744 4020 2279
## SP7 0 0 1 1 0 0
## MUCL1 0 0 0 0 0 0
## CD63 3052 2432 3575 3903 3376 1024
## SUOX 967 974 935 1162 1039 286
## RPS26 3989 3150 4434 3683 4384 423
## RPL41 7794 6331 9553 7003 9350 3817
## IL23A 42 41 31 26 48 34
## DDIT3 495 756 913 927 846 270
## IFNG 7 26 20 144 35 1
## IL22 0 0 0 0 1 0
## LYZ 82162 77797 122045 51530 41655 15415
## CAPS2 6 5 4 6 4 1
## SYT1 4 1 0 0 2 1
## BTG1 14369 9551 13082 12777 11302 2817
## HCAR3 694 1163 1113 1275 1520 318
## GJB2 0 1 7 2 4 0
## GJB6 28 14 40 39 50 11
## TNFSF11 10 4 4 2 4 2
## TPT1 59325 47023 66046 50353 66883 20924
## LMO7 84 81 51 30 52 42
## TNFSF13B 1135 2546 1862 1740 2246 537
## LAMP1 2808 2488 2894 2922 3160 876
## PSME2 1507 1083 1591 1445 1571 410
## GZMB 828 693 1429 1716 1066 124
## RPL36AL 2945 1853 2953 2562 3005 1015
## PYGL 3041 4367 4106 5541 4540 1030
## HIF1A 3529 2544 4196 2657 2517 443
## FOS 7685 44038 41457 56001 46903 6362
## JDP2 1161 852 1000 1045 1073 168
## NOXRED1 3 8 8 6 13 1
## SERPINA1 18766 22005 24615 24077 30959 5794
## CDC42BPB 295 209 188 157 260 51
## PLA2G4D 1 0 0 0 0 0
## TRIM69 13 18 9 10 12 12
## SLC51B 0 0 0 0 0 0
## SMAD3 995 612 797 529 663 238
## CYP1A1 0 0 2 1 0 0
## AKAP13 5178 3035 4110 2999 2799 842
## MEFV 1760 2846 2210 2869 2508 495
## SOCS1 85 51 97 54 90 32
## ATXN2L 1858 1892 1892 1653 1824 514
## CD19 64 117 65 44 71 127
## ITGAL 5788 4512 5594 5089 5402 1716
## ITGAM 4444 4466 5132 5069 4645 1173
## ITGAX 4337 6028 6049 5992 6446 1040
## DNAJA2 741 606 781 639 663 200
## SIAH1 217 133 182 150 113 37
## ADCY7 2359 2512 1994 1962 2148 429
## NOD2 551 1126 1071 439 902 102
## CMTM2 1064 2350 1893 2539 2732 536
## SF3B3 785 792 736 728 672 315
## PSMD7 941 693 980 823 888 334
## WWOX 53 35 51 45 37 20
## MAF 496 425 447 457 506 147
## SLC7A5 768 315 472 320 482 42
## CXCL16 1880 2421 2433 2798 3037 319
## XAF1 519 860 531 835 827 151
## CD68 4461 3999 5339 5260 4352 855
## PER1 3863 709 1870 1331 1046 398
## NOS2 5 0 3 3 2 0
## TRAF4 98 133 149 55 123 55
## CCL2 2 3 10 9 4 0
## CCL5 4962 2557 4294 7944 5621 1530
## CCL3 34 160 201 284 163 65
## CCR7 1094 631 563 168 447 663
## STAT3 3920 4441 3567 4322 3913 1005
## SOST 0 0 0 0 0 0
## ITGA2B 604 254 499 332 295 133
## EFCAB13 17 33 24 9 10 5
## NPEPPS 838 847 729 957 776 178
## TBX21 457 328 460 724 585 50
## COL1A1 1 2 2 0 4 1
## MRPS23 198 135 186 147 170 53
## MIR21 5 7 6 7 7 1
## RPS6KB1 438 297 310 295 301 117
## ACE 117 53 52 32 61 24
## ERN1 1928 1021 1268 1131 1466 300
## PRTN3 2 6 9 15 12 44
## PLIN5 72 116 78 77 125 54
## RETN 50 104 85 75 96 136
## CCL25 0 1 2 0 0 0
## ICAM1 1365 1802 2408 1622 2746 293
## TYK2 1628 1868 1715 1795 1867 664
## SMARCA4 753 686 778 579 655 468
## ACP5 329 186 442 272 402 164
## JUNB 15185 43478 40710 41202 56317 6655
## CYP4F22 28 23 32 25 21 4
## JAK3 1890 1879 1717 1440 2553 1606
## JUND 4835 7293 9571 8371 9836 3938
## CEBPA 962 906 1227 1104 1078 292
## CEBPG 348 258 372 299 299 80
## ACP7 0 1 0 0 0 0
## ZFP36 8870 23332 30000 23815 33685 2151
## TGFB1 5995 5502 6598 6351 7121 1509
## RPS19 11404 9087 11256 9069 11812 8142
## PSG2 0 0 0 0 0 0
## FUT2 1 2 4 2 4 4
## NKG7 3700 2747 4655 7222 4843 696
## ZNF415 3 3 8 1 3 0
## LILRB2 4069 4769 4512 4190 5216 825
## LILRA5 1285 2886 2500 3060 2541 1363
## KIR3DL1 60 105 61 69 218 6
## KIR3DL2 157 71 122 52 83 7
## SMOX 122 123 146 120 122 111
## BMP2 5 4 7 2 3 3
## GINS1 5 13 8 8 7 1
## PLCG1 1077 776 688 411 731 403
## YWHAB 5480 4799 6280 6363 5808 2125
## PI3 605 306 933 1674 740 741
## MMP9 1055 1927 783 3435 1633 904
## CD40 140 173 120 142 184 61
## PFDN4 56 43 63 62 72 28
## BMP7 0 0 0 0 0 0
## RPS21 4979 4053 5783 4178 5836 2895
## MX1 432 1824 914 1665 767 169
## PFKL 1187 1211 1191 1024 1132 509
## IL17RA 5112 4555 3907 4909 4612 1260
## UBE2L3 951 884 1098 1214 1024 355
## TPST2 1394 1184 1318 1549 1310 298
## XBP1 1789 924 1306 1411 1581 303
## UQCR10 541 482 625 550 594 268
## SEC14L2 56 38 47 13 77 28
## APOL6 1404 1130 1150 931 793 295
## APOL1 468 467 515 508 574 117
## TYMP 2848 4202 4733 4531 5269 2666
## BEND2 51 57 44 60 60 24
## PHEX 6 12 8 5 7 0
## TIMP1 1713 2160 1838 1844 2427 736
## FOXP3 119 100 110 39 64 25
## MSN 23284 23371 23149 25434 25291 4407
## PGK1 6926 7260 8103 7559 8456 1428
## LAMP2 5543 6015 5828 6937 6483 999
## CD40LG 348 132 148 127 200 63
## IRAK1 1978 1494 1708 1412 1738 375
## COX2 64192 50557 68548 49585 68176 618605
## GSM3308449 GSM3308450 GSM3308451 GSM3308452 GSM3308453 GSM3308454
## TNFRSF9 27 53 115 58 128 78
## ENO1 1357 7300 6575 4805 6118 5685
## PIK3CD 2009 4433 6326 4731 7073 4864
## PGD 1327 4080 4807 5566 4553 3454
## MTHFR 105 490 519 332 640 403
## TNFRSF1B 3177 10040 14510 9137 14386 11891
## PINK1 250 383 782 483 686 616
## IFNLR1 12 33 39 31 55 66
## RUNX3 757 3336 3790 3052 3779 4778
## SH3BGRL3 4222 8038 9290 9045 10097 9312
## CD52 1141 4531 3633 4650 4499 5156
## IFI6 348 889 1167 1820 2029 3452
## ZC3H12A 76 573 709 611 650 655
## UTP11 21 97 77 38 63 76
## JUN 3323 13631 10703 11634 27441 23029
## KANK4 0 0 0 0 0 0
## EFCAB7 4 27 36 13 27 19
## IL23R 0 4 2 2 7 0
## ADGRL2 0 0 0 0 0 0
## GBP3 30 442 232 69 451 73
## GBP1 114 1853 939 362 1917 881
## GBP5 280 6204 3030 1644 5461 3173
## TGFBR3 131 821 858 469 817 1117
## VCAM1 0 4 4 0 1 3
## PTPN22 49 421 386 293 304 328
## CD160 28 179 159 48 76 83
## FCGR1A 122 2057 487 712 1599 980
## MCL1 5266 29112 32144 20046 25174 20895
## CTSK 7 73 68 58 46 50
## RORC 12 190 10 28 73 50
## S100A9 25603 67773 96288 77156 96692 83363
## S100A12 793 2194 3453 1727 2550 1775
## S100A8 13625 25815 35110 29348 38916 31437
## IL6R 677 3127 4068 2050 4336 2442
## RIT1 232 1393 1602 1317 1030 1151
## BGLAP 3 6 7 5 8 6
## IFI16 328 1733 2107 857 2891 2082
## AIM2 22 133 115 29 153 148
## CRP 0 0 0 0 0 0
## FCGR2A 1927 9362 11018 8141 12218 9240
## HSPA6 550 1020 1670 1010 1720 1119
## FCGR3A 1688 12990 15635 8824 16739 7326
## SELL 5395 30026 33539 21601 36535 24126
## GLUL 2732 15393 18196 13888 13377 16038
## PTGS2 1877 13311 10002 7709 15900 11698
## CRB1 0 1 4 0 2 0
## KDM5B 73 502 583 384 438 409
## IL10 1 6 6 6 3 3
## YOD1 38 455 1798 226 269 226
## HHAT 7 37 47 20 34 46
## TRAF5 92 427 453 174 472 370
## NLRP3 78 1267 1124 660 903 1158
## LINC01250 0 0 1 0 0 0
## RPS7 2349 10215 6528 5646 9079 9139
## RSAD2 64 528 1101 678 999 2700
## FOSL2 490 4825 6043 4445 4220 4567
## REL 115 1677 1601 681 1155 1278
## TGFA 102 451 646 596 443 427
## DYSF 807 3348 4321 3007 5666 3346
## HK2 143 1465 1096 1882 956 932
## CD8A 340 1481 1238 837 1663 1576
## CD8B 138 634 401 435 945 768
## EIF5B 242 637 491 317 464 451
## IL1R1 39 298 223 163 209 185
## RGPD6 19 114 167 60 88 72
## IL1A 1 1 2 2 0 0
## IL1B 174 925 804 742 1238 976
## IL37 0 0 0 0 0 0
## IL36RN 0 0 0 0 0 0
## IL1F10 0 0 0 0 0 0
## IL1RN 1083 1589 2369 2435 3895 3969
## NMI 273 1170 1111 795 1406 1156
## TNFAIP6 29 271 251 174 332 453
## IFIH1 54 458 453 259 637 515
## SCN1A 0 0 0 0 0 0
## ABCB11 0 0 2 0 3 2
## RBM45 9 48 73 25 47 58
## FRZB 0 0 0 0 0 0
## TFPI 10 4 12 3 2 1
## STAT1 504 6371 4941 2001 6467 3901
## NABP1 186 790 1641 422 691 503
## SF3B1 553 5960 6630 3374 4771 4068
## CASP10 58 488 522 181 376 265
## CD28 79 1479 1016 515 812 794
## CTLA4 25 103 86 48 76 83
## ICOS 30 288 242 140 139 216
## NDUFS1 85 634 640 278 444 413
## CXCR2 2683 10228 13276 9126 18726 13991
## IRS1 19 162 50 82 109 96
## CCL20 0 2 1 1 4 2
## ATG16L1 61 348 348 266 328 285
## GPR35 28 112 131 225 121 99
## PDCD1 9 29 27 23 40 54
## PPARG 0 8 1 4 2 3
## RPL15 2957 14909 11791 8979 15287 14268
## EOMES 25 135 209 47 132 135
## CX3CR1 117 872 918 260 912 600
## ACKR2 1 1 1 4 1 0
## CCR2 36 761 878 180 544 302
## CCRL2 7 68 56 35 49 50
## TLR9 21 74 58 54 59 44
## ARHGEF3 206 1702 1259 717 1336 1102
## ADAMTS9 0 0 0 0 0 0
## TMEM45A 1 0 1 1 1 1
## CD80 2 15 13 10 1 6
## CD86 70 1235 865 407 843 709
## MIX23 3 32 28 8 16 19
## PLS1 4 36 22 11 14 24
## PTX3 12 90 52 57 72 51
## GOLIM4 3 136 102 104 69 69
## MYNN 42 424 442 238 316 320
## TNFSF10 258 2249 2288 1063 3516 2044
## ADIPOQ 0 1 0 0 0 0
## SPON2 243 277 726 200 343 630
## S100P 732 1456 3052 1491 1594 1165
## WDR1 1264 4562 5095 3922 4801 4511
## CD38 33 320 278 71 288 208
## PPARGC1A 0 10 6 0 2 1
## TMPRSS11B 0 0 0 0 0 0
## CSN3 0 0 0 0 0 0
## ALB 0 0 1 0 0 0
## CXCL8 8302 45990 45998 52752 42605 73489
## CXCL2 11 8 12 29 18 45
## AREG 10 66 75 141 26 158
## CXCL10 0 33 18 1 58 12
## CXCL13 0 5 1 0 0 0
## SPP1 4 39 47 40 11 84
## HERC6 36 220 263 151 249 281
## NFKB1 109 1048 1084 667 838 867
## SEC24B 91 597 604 362 517 378
## EGF 35 53 46 32 16 9
## IL2 0 0 0 0 0 0
## IL21 0 0 0 0 0 0
## IL21-AS1 0 0 0 0 1 1
## SLC7A11 2 12 22 25 10 8
## IL15 20 79 84 24 73 59
## EDNRA 0 0 0 0 0 0
## TLR2 652 3341 4281 1803 3490 2740
## FGB 0 0 0 0 0 0
## DDX60 47 497 892 296 620 696
## SPCS3 316 2785 2320 1049 1477 1602
## TLR3 2 17 11 6 10 7
## OSMR 3 60 83 25 42 38
## GZMK 164 718 1073 262 697 1007
## GZMA 270 1094 1157 595 1030 1299
## ANKRD55 17 61 100 77 136 36
## CENPK 1 47 105 25 105 36
## CAST 421 2959 2452 1247 3252 2221
## ERAP1 211 1436 1500 838 1196 1087
## ERAP2 353 315 1452 1060 2086 2785
## TNFAIP8 254 1905 1577 886 1221 1253
## CSF2 0 2 0 1 0 0
## IL5 0 2 1 0 0 0
## IL13 0 2 0 0 0 0
## IL4 2 4 7 0 7 1
## CD14 957 6450 7644 5646 8512 8943
## CSNK1A1 394 1535 1471 999 1403 1305
## PPARGC1B 14 256 152 73 171 111
## TNIP1 961 2733 4019 3292 4609 3852
## ATOX1 104 193 133 113 187 149
## FAXDC2 170 182 259 117 151 101
## IL12B 0 0 0 1 0 0
## MIR146A 0 0 1 0 0 0
## PDLIM7 560 711 1328 1315 1397 1339
## SERPINB1 1071 3285 3617 2974 4377 3517
## SSR1 245 2936 2291 1318 1900 1783
## CD83 144 932 769 436 949 983
## SOX4 28 184 201 66 141 93
## CMAHP 28 113 149 105 117 95
## HLA-A 12554 37983 45656 38465 36022 45446
## HLA-C 17374 38147 74638 60544 98151 62314
## HLA-B 29617 76749 91139 90256 117542 102496
## MICA 27 173 142 87 212 155
## LTA 23 55 42 50 101 71
## TNF 17 271 114 84 283 173
## HLA-DRB1 636 6440 3149 1736 4351 4251
## HLA-DQB1 191 1654 851 152 220 566
## PPARD 84 280 315 215 327 302
## CCND3 1722 3606 3423 4673 4561 4260
## VEGFA 25 218 201 377 234 199
## RUNX2 110 1031 554 567 475 590
## IL17A 0 5 1 1 0 0
## IL17F 0 2 0 0 0 0
## PRDM1 157 686 557 425 493 539
## ATG5 77 459 413 335 352 398
## TRAF3IP2 40 174 160 174 205 199
## NCOA7 54 603 373 216 391 411
## SGK1 296 4020 2881 4203 2668 3636
## IFNGR1 404 2088 2817 1665 1769 1716
## TNFAIP3 790 7927 6403 4604 6695 9336
## SOD2 6709 33968 49812 23071 44756 25461
## LPAL2 9 20 27 4 14 19
## PLG 0 0 1 1 0 0
## CCR6 20 277 95 44 96 96
## RAC1 563 2385 2519 1748 2401 2110
## ZNF316 234 653 891 684 907 851
## AHR 65 1877 1352 714 1154 735
## IL6 3 6 9 12 7 8
## TOMM7 689 2498 2017 1836 2297 1853
## CYCS 136 1006 702 465 684 652
## AQP1 2 4 10 2 5 2
## NT5C3A 296 664 721 520 763 614
## EGFR 0 0 0 0 0 0
## CD36 174 2859 2840 1210 2263 1757
## SAMD9 175 1964 2306 852 2273 1871
## SERPINE1 13 7 11 8 4 7
## CUX1 333 1705 2051 1097 1880 1363
## PSMC2 55 420 311 203 268 273
## NAMPT 5347 41974 54764 34930 37058 36594
## HYAL4 0 0 0 0 0 0
## LEP 1 1 2 2 1 2
## CALD1 32 11 21 8 10 7
## BRAF 114 763 960 653 751 727
## EZH2 10 94 51 44 59 64
## DNAJB6 426 1399 1369 1146 1143 1132
## CSMD1 0 0 6 0 9 0
## CTSB 649 6076 5891 3206 4642 3996
## EGR3 124 335 383 499 565 605
## TNFRSF10A 19 236 213 113 213 166
## BNIP3L 322 1955 5038 1105 1696 1436
## DUSP4 14 102 45 79 62 74
## NRG1 6 32 125 91 96 97
## RPL7 3129 14647 8689 7050 11438 10131
## IL7 5 24 23 2 10 11
## GEM 0 1 3 5 0 3
## MYC 133 516 541 384 544 314
## GPT 3 2 4 1 6 3
## JAK2 104 1442 1464 916 1292 908
## CD274 17 345 175 138 274 140
## IL33 0 0 0 0 0 0
## LURAP1L-AS1 0 0 0 0 0 0
## LURAP1L 4 2 4 1 4 1
## TTC39B 57 333 346 57 227 102
## IFNA1 0 0 0 0 0 0
## TEK 6 12 61 7 8 22
## TRBV20OR9-2 0 1 0 0 0 0
## TOMM5 68 254 176 139 202 181
## ANXA1 709 11744 6290 8417 5383 5769
## ERP44 229 1465 1286 879 1542 1106
## ZNF483 6 45 137 33 44 38
## TNFSF15 0 2 9 1 6 2
## TLR4 597 5784 6107 2575 7407 4968
## PTGS1 799 887 891 838 545 416
## HSPA5 1028 8341 4656 4887 6317 6764
## FNBP1 603 3373 2877 2135 3308 2833
## CARD9 39 167 176 79 236 84
## TRAF2 49 117 145 86 116 144
## CLIC3 76 62 131 46 98 105
## IL2RA 40 150 90 228 86 140
## GATA3 144 300 274 178 301 297
## VIM 2936 17449 15274 11756 12787 12691
## CREM 44 207 189 141 144 277
## DKK1 0 0 1 0 0 0
## MBL2 0 0 0 0 0 0
## SAR1A 184 1024 1196 703 782 764
## PRF1 661 1868 2360 1051 1831 2066
## ZMIZ1 267 2801 2944 2530 2925 2353
## IFIT3 738 5517 4178 4433 9678 12550
## TALDO1 3044 5602 8214 6568 8108 6335
## IGF2 0 0 2 0 0 0
## INS-IGF2 0 0 2 0 0 0
## IGF2-AS 0 0 0 0 0 0
## INS 0 0 0 0 0 0
## STIM1 235 1246 1203 958 1299 1326
## TRIM22 379 2785 3159 1510 3100 2824
## PTH 0 0 0 0 0 0
## SAA1 0 0 0 1 1 0
## SLC1A2 0 3 4 2 1 2
## FOSL1 22 84 40 146 45 109
## CCND1 2 9 10 2 3 4
## JRKL 25 99 72 34 76 60
## MMP7 0 0 0 0 0 0
## MMP1 7 6 2 0 0 0
## MMP3 0 0 0 0 0 0
## CASP1 470 3196 2428 1437 3295 2167
## DLAT 32 175 143 73 185 137
## IL18 14 79 81 54 72 61
## CD3E 825 3327 2451 2183 3762 3323
## MCAM 63 312 248 214 290 244
## WNK1 478 4219 4120 2469 4790 3996
## TNFRSF1A 947 2370 2930 1671 4236 2264
## GAPDH 3187 17564 16166 13221 17814 15696
## CD4 353 5120 3805 2356 4290 3295
## SLC2A3 1692 7164 13068 8350 7380 9157
## CLEC4D 97 248 274 117 498 186
## KLRB1 169 1595 678 372 736 921
## CD69 701 4203 3137 4226 2730 3613
## CLEC2B 597 1813 1512 1168 1896 1776
## OLR1 5 13 9 17 8 20
## ABCD2 15 357 495 109 232 195
## LRRK2 682 7568 12560 3500 8923 5278
## VDR 104 363 383 376 342 215
## TMBIM6 2253 11529 12373 8176 12355 10450
## PFDN5 1086 3954 2792 2386 3318 3074
## SP7 0 0 1 0 1 0
## MUCL1 0 0 0 0 0 0
## CD63 983 2571 2483 3550 2229 2709
## SUOX 294 769 855 623 913 745
## RPS26 279 6217 3094 2808 712 4048
## RPL41 2559 6831 6059 5718 8263 8779
## IL23A 7 73 49 35 53 59
## DDIT3 314 708 688 607 509 437
## IFNG 14 58 53 39 93 94
## IL22 0 1 1 1 1 1
## LYZ 6529 95893 64568 58632 88140 28068
## CAPS2 1 9 16 4 6 13
## SYT1 2 6 9 0 3 2
## BTG1 3636 10240 9857 8534 9580 11095
## HCAR3 475 1727 2085 1170 4265 2343
## GJB2 0 1 3 0 1 0
## GJB6 9 21 51 14 17 11
## TNFSF11 0 2 8 0 3 1
## TPT1 11528 67676 41529 37672 58292 51586
## LMO7 11 99 91 42 98 78
## TNFSF13B 524 2042 2379 1528 2640 2070
## LAMP1 703 2418 3024 2033 3080 2405
## PSME2 258 2106 912 803 1961 1232
## GZMB 307 635 1044 678 931 1167
## RPL36AL 770 2654 1909 1797 2549 2268
## PYGL 792 3117 4797 4279 4558 3269
## HIF1A 220 4138 3924 5103 2065 2906
## FOS 13062 70672 55320 71693 116448 60188
## JDP2 144 571 702 672 642 600
## NOXRED1 3 5 15 4 7 9
## SERPINA1 4405 20313 17113 17232 25482 17226
## CDC42BPB 35 248 219 130 318 218
## PLA2G4D 0 0 0 0 0 0
## TRIM69 10 15 12 10 12 21
## SLC51B 0 0 0 0 0 0
## SMAD3 141 820 668 625 624 862
## CYP1A1 0 1 1 0 0 0
## AKAP13 679 7171 6271 3586 5789 4669
## MEFV 450 2008 2552 1402 2535 1979
## SOCS1 46 92 141 167 127 139
## ATXN2L 323 1565 1631 1287 2546 1763
## CD19 57 75 81 41 138 197
## ITGAL 1438 5571 5250 4091 5954 5472
## ITGAM 948 4394 5015 6564 5941 4392
## ITGAX 1200 4423 4591 4954 5275 4194
## DNAJA2 127 718 650 401 536 574
## SIAH1 34 157 299 137 113 114
## ADCY7 235 2412 2527 1242 3242 2180
## NOD2 103 632 531 901 641 770
## CMTM2 726 1177 1505 951 1524 1670
## SF3B3 174 1087 1001 502 1017 917
## PSMD7 199 813 800 572 643 611
## WWOX 8 55 52 25 52 48
## MAF 99 702 452 387 502 572
## SLC7A5 39 209 311 263 266 211
## CXCL16 421 1489 2084 1875 2045 1567
## XAF1 166 1069 784 751 1567 1566
## CD68 336 4438 3563 1848 3643 2991
## PER1 521 1091 1074 1152 637 998
## NOS2 1 0 2 0 2 5
## TRAF4 28 114 84 101 110 116
## CCL2 0 22 16 32 39 18
## CCL5 2350 2459 4442 2880 4782 5910
## CCL3 127 339 307 129 580 281
## CCR7 114 715 956 432 982 627
## STAT3 900 3660 4254 2506 4456 3568
## SOST 0 0 1 0 0 0
## ITGA2B 720 458 433 735 190 177
## EFCAB13 5 39 71 12 29 31
## NPEPPS 142 713 903 448 794 586
## TBX21 162 312 387 195 350 383
## COL1A1 0 2 1 1 0 2
## MRPS23 25 145 133 85 102 116
## MIR21 1 3 9 2 3 4
## RPS6KB1 55 453 439 185 372 333
## ACE 11 96 34 27 57 99
## ERN1 263 1438 1194 631 1192 1273
## PRTN3 10 1 14 32 6 22
## PLIN5 99 35 84 71 74 98
## RETN 35 42 45 74 94 51
## CCL25 0 0 1 1 2 0
## ICAM1 269 2202 2266 1723 2209 1537
## TYK2 558 1158 1696 992 1977 1172
## SMARCA4 153 655 702 454 822 674
## ACP5 78 212 297 243 239 376
## JUNB 6875 14364 30448 31767 40361 36681
## CYP4F22 5 32 51 9 13 15
## JAK3 1130 1481 1981 1359 2262 1545
## JUND 8145 5683 10923 13363 15719 15514
## CEBPA 184 525 906 395 781 408
## CEBPG 39 397 356 161 240 267
## ACP7 0 0 0 0 0 0
## ZFP36 4950 19016 24419 33030 34949 38595
## TGFB1 1425 3049 4595 4621 5528 4884
## RPS19 4515 10811 9687 7693 11605 12425
## PSG2 0 0 0 0 0 0
## FUT2 2 2 3 1 6 4
## NKG7 1567 2725 4145 2787 4136 5925
## ZNF415 1 3 7 1 11 11
## LILRB2 622 3233 4167 3405 4734 3536
## LILRA5 854 1031 2834 1881 3081 1385
## KIR3DL1 19 36 62 13 78 74
## KIR3DL2 17 46 92 25 66 53
## SMOX 212 121 169 106 64 62
## BMP2 2 5 10 4 9 4
## GINS1 2 8 5 3 12 5
## PLCG1 168 1129 828 458 1038 764
## YWHAB 1470 6209 5230 3628 5740 5075
## PI3 507 300 603 1786 1332 897
## MMP9 718 715 1546 1188 2650 1095
## CD40 47 199 128 75 156 177
## PFDN4 25 62 66 34 52 49
## BMP7 0 0 1 0 0 0
## RPS21 1675 4539 3689 3372 5219 5113
## MX1 359 774 1264 1476 2647 3512
## PFKL 243 1123 1106 679 1273 1106
## IL17RA 1070 3433 4532 3372 6313 4028
## UBE2L3 235 880 794 696 973 779
## TPST2 374 914 1242 1037 1242 1289
## XBP1 155 1161 1034 692 771 958
## UQCR10 163 557 467 403 517 409
## SEC14L2 2 45 45 17 65 24
## APOL6 282 3388 2886 809 2733 1731
## APOL1 129 960 629 352 1188 456
## TYMP 1620 2361 2893 2237 6635 3402
## BEND2 64 81 74 29 28 8
## PHEX 1 20 14 9 15 17
## TIMP1 660 1296 1295 1090 1105 1918
## FOXP3 39 89 48 47 89 110
## MSN 3732 23134 22106 17165 24087 22416
## PGK1 836 8643 7714 6487 7031 6243
## LAMP2 808 5675 7219 4188 5567 4880
## CD40LG 24 282 127 76 194 136
## IRAK1 225 1491 1436 1257 1664 1486
## COX2 136097 54310 47314 48572 61407 42088
## GSM3308455 GSM3308456 GSM3308457 GSM3308458 GSM3308459 GSM3308460
## TNFRSF9 171 56 21 76 125 83
## ENO1 6844 4057 2065 5220 5229 6741
## PIK3CD 7189 4870 3539 5226 5532 6723
## PGD 6152 3574 2569 4014 6170 4097
## MTHFR 675 405 130 423 301 683
## TNFRSF1B 16775 9584 5269 13269 11950 13896
## PINK1 870 573 426 741 840 673
## IFNLR1 79 33 20 70 56 85
## RUNX3 4051 2816 660 6894 2144 4168
## SH3BGRL3 13172 6335 9410 11034 9351 9371
## CD52 4505 2712 1559 6010 2661 3654
## IFI6 932 858 4948 1351 1497 1124
## ZC3H12A 754 135 71 672 415 440
## UTP11 66 69 37 78 54 93
## JUN 20323 1320 348 20068 5658 5071
## KANK4 1 0 0 0 0 1
## EFCAB7 28 22 10 21 23 28
## IL23R 0 4 0 5 4 2
## ADGRL2 0 0 0 0 0 0
## GBP3 89 146 65 140 197 206
## GBP1 671 647 412 1053 900 1079
## GBP5 2219 1772 572 4360 4376 3372
## TGFBR3 1108 579 72 1217 295 943
## VCAM1 6 1 0 4 0 0
## PTPN22 282 333 45 332 251 469
## CD160 99 95 18 131 77 109
## FCGR1A 741 225 388 829 1062 682
## MCL1 28602 15873 6216 22083 29429 21974
## CTSK 71 35 4 60 28 66
## RORC 32 31 10 53 38 39
## S100A9 143859 50814 50839 64526 148159 55804
## S100A12 6059 1483 1829 1460 3384 1425
## S100A8 60418 18834 21795 22682 55687 20879
## IL6R 4670 3262 1091 2818 4077 3719
## RIT1 1613 806 273 1425 1538 1098
## BGLAP 8 3 6 5 5 6
## IFI16 1794 2226 904 1390 3014 2472
## AIM2 88 69 42 103 259 107
## CRP 0 0 0 0 0 0
## FCGR2A 11451 7834 2046 8011 12979 9756
## HSPA6 1458 926 1318 1250 1872 1126
## FCGR3A 9118 13429 2364 15899 22838 16908
## SELL 35112 18968 8161 32776 45843 20504
## GLUL 16972 7911 4082 12457 11283 10618
## PTGS2 16565 2448 1193 4810 7389 7621
## CRB1 2 1 0 2 0 2
## KDM5B 487 316 92 385 482 409
## IL10 2 2 0 5 9 5
## YOD1 227 171 39 284 326 316
## HHAT 37 27 3 50 27 53
## TRAF5 265 248 115 344 226 484
## NLRP3 1525 543 66 720 664 891
## LINC01250 0 1 0 0 0 1
## RPS7 7204 4845 2591 12050 6082 8840
## RSAD2 275 455 2043 593 671 527
## FOSL2 4395 1721 482 4923 2902 3467
## REL 1193 923 93 1267 928 1287
## TGFA 353 340 97 396 685 364
## DYSF 6128 2730 881 2455 6672 3676
## HK2 1559 585 182 765 1072 1004
## CD8A 3108 895 208 810 1018 1682
## CD8B 1310 394 137 333 578 595
## EIF5B 354 366 249 476 297 553
## IL1R1 243 152 35 236 294 221
## RGPD6 48 73 12 73 49 81
## IL1A 1 0 0 0 0 0
## IL1B 846 154 261 197 217 471
## IL37 0 0 0 0 0 0
## IL36RN 0 0 0 0 0 0
## IL1F10 0 0 0 0 0 0
## IL1RN 3220 892 2802 2073 2178 2093
## NMI 1300 820 628 1171 1779 1148
## TNFAIP6 428 435 110 167 659 463
## IFIH1 362 285 170 338 390 449
## SCN1A 0 0 0 0 0 0
## ABCB11 2 2 0 0 0 2
## RBM45 38 49 18 43 29 70
## FRZB 0 0 0 0 0 0
## TFPI 1 3 22 3 3 0
## STAT1 3628 2666 1238 3727 3536 4601
## NABP1 580 353 187 309 657 610
## SF3B1 4433 2855 412 3796 3689 5046
## CASP10 260 302 97 319 256 373
## CD28 345 262 92 853 243 650
## CTLA4 78 22 14 110 40 72
## ICOS 112 74 43 210 59 144
## NDUFS1 466 438 102 408 421 528
## CXCR2 11372 13483 3395 9838 19712 11693
## IRS1 56 38 53 107 80 117
## CCL20 4 0 3 7 6 2
## ATG16L1 279 170 78 323 193 368
## GPR35 130 26 23 125 88 115
## PDCD1 44 66 7 39 25 28
## PPARG 9 4 1 6 5 2
## RPL15 12575 8820 3858 19454 10129 14545
## EOMES 137 144 55 141 72 150
## CX3CR1 1343 1397 238 381 424 2183
## ACKR2 2 2 0 0 0 3
## CCR2 625 845 66 345 618 654
## CCRL2 30 33 15 30 34 33
## TLR9 54 38 48 63 82 53
## ARHGEF3 1230 721 206 996 635 1170
## ADAMTS9 0 0 0 0 0 0
## TMEM45A 4 1 11 2 7 1
## CD80 4 3 1 5 3 4
## CD86 905 828 85 919 576 1077
## MIX23 17 18 9 15 11 20
## PLS1 8 11 1 21 7 21
## PTX3 121 9 7 63 36 105
## GOLIM4 66 84 7 76 62 102
## MYNN 273 200 54 336 292 339
## TNFSF10 2178 2517 667 1596 2670 2458
## ADIPOQ 0 0 0 0 0 0
## SPON2 383 469 339 1370 276 677
## S100P 4830 2056 179 3567 4437 1373
## WDR1 6117 3864 2345 4802 4984 5777
## CD38 149 252 45 370 189 308
## PPARGC1A 6 3 0 1 10 4
## TMPRSS11B 0 0 0 0 0 0
## CSN3 0 0 0 0 0 0
## ALB 0 0 0 0 1 0
## CXCL8 91307 4435 1002 58664 28348 31644
## CXCL2 50 5 5 10 19 10
## AREG 68 43 2 232 216 68
## CXCL10 12 10 2 15 12 34
## CXCL13 0 0 0 2 0 0
## SPP1 48 16 1 88 11 116
## HERC6 143 170 194 166 150 205
## NFKB1 699 646 118 794 612 861
## SEC24B 412 385 82 438 375 450
## EGF 51 29 176 27 36 23
## IL2 1 1 1 1 0 1
## IL21 0 1 0 1 2 3
## IL21-AS1 1 1 0 1 1 2
## SLC7A11 18 4 3 17 7 15
## IL15 94 73 17 56 52 67
## EDNRA 0 0 0 0 0 0
## TLR2 4634 3293 712 2577 8913 3056
## FGB 0 0 0 0 0 0
## DDX60 295 375 262 323 342 433
## SPCS3 1629 1472 422 1471 1640 2039
## TLR3 9 14 0 12 3 15
## OSMR 34 20 0 27 22 45
## GZMK 702 356 48 978 440 722
## GZMA 1445 883 253 1477 550 1138
## ANKRD55 47 66 29 115 96 98
## CENPK 77 45 4 73 71 24
## CAST 3602 2820 643 1784 2304 2783
## ERAP1 2069 1117 192 1819 1571 1522
## ERAP2 160 121 168 1842 163 2118
## TNFAIP8 935 848 332 1281 1013 1337
## CSF2 0 0 0 1 0 1
## IL5 0 0 0 1 0 0
## IL13 0 1 0 0 1 1
## IL4 2 1 0 2 0 12
## CD14 10796 3123 1403 5649 6901 8134
## CSNK1A1 1425 1239 675 1269 1324 1532
## PPARGC1B 139 93 13 133 117 260
## TNIP1 5357 2717 1762 3824 5265 4097
## ATOX1 173 146 150 159 142 195
## FAXDC2 151 134 504 194 96 175
## IL12B 1 0 0 0 1 2
## MIR146A 0 0 0 1 0 0
## PDLIM7 2135 817 944 1339 1582 1110
## SERPINB1 4266 2901 2020 2988 4276 3049
## SSR1 2157 1553 375 1978 2038 2381
## CD83 969 54 36 804 210 1069
## SOX4 206 166 88 244 158 284
## CMAHP 64 28 40 78 49 117
## HLA-A 40930 33811 23078 61099 44929 38608
## HLA-C 100979 56611 20105 102535 62214 59345
## HLA-B 89597 69694 28025 115037 103222 89831
## MICA 116 97 82 105 108 192
## LTA 44 39 26 55 22 76
## TNF 167 21 34 189 65 258
## HLA-DRB1 3816 4763 587 6509 1979 7286
## HLA-DQB1 302 1454 208 1675 259 1666
## PPARD 241 208 86 392 226 320
## CCND3 4461 3295 3641 6087 7379 3800
## VEGFA 231 104 18 285 151 192
## RUNX2 562 355 92 784 590 506
## IL17A 0 0 0 0 0 0
## IL17F 0 0 0 0 0 0
## PRDM1 698 785 143 1040 939 586
## ATG5 342 240 63 428 332 388
## TRAF3IP2 157 107 75 250 179 204
## NCOA7 303 287 103 346 299 384
## SGK1 4036 2076 270 1452 2008 2661
## IFNGR1 2096 2881 406 1771 4214 2262
## TNFAIP3 6952 2588 166 8263 9672 3603
## SOD2 46517 22619 6833 30687 36424 36188
## LPAL2 14 4 2 13 13 19
## PLG 0 0 0 0 0 1
## CCR6 44 74 68 116 33 110
## RAC1 2782 1879 2120 2560 2443 2639
## ZNF316 799 402 289 851 578 665
## AHR 1238 718 61 855 960 1240
## IL6 4 2 1 4 2 5
## TOMM7 1946 1267 877 3552 1742 2506
## CYCS 668 368 122 679 421 660
## AQP1 5 1 10 3 5 5
## NT5C3A 627 414 917 674 741 598
## EGFR 0 0 0 0 0 0
## CD36 4296 2002 250 1517 2265 2572
## SAMD9 1494 1198 432 1117 1916 1906
## SERPINE1 7 15 14 12 6 14
## CUX1 2110 1349 503 1713 1701 2216
## PSMC2 329 257 77 341 206 347
## NAMPT 50943 23177 5259 35418 62489 32898
## HYAL4 0 0 0 0 0 1
## LEP 2 2 4 7 3 6
## CALD1 23 13 67 24 1 19
## BRAF 795 472 125 679 576 861
## EZH2 39 43 8 66 35 74
## DNAJB6 1356 878 693 1357 1283 1354
## CSMD1 0 3 0 4 0 17
## CTSB 5421 4227 1221 6010 5011 5388
## EGR3 645 53 116 255 232 359
## TNFRSF10A 111 70 21 153 108 176
## BNIP3L 2149 1601 558 1672 1957 2030
## DUSP4 82 10 6 185 20 49
## NRG1 301 127 17 155 125 163
## RPL7 8357 6449 4489 14071 7488 11016
## IL7 13 11 6 7 9 18
## GEM 0 1 0 2 0 0
## MYC 307 651 212 592 574 622
## GPT 1 4 0 2 1 4
## JAK2 1310 821 158 759 1419 942
## CD274 94 63 34 181 220 107
## IL33 0 0 0 0 0 0
## LURAP1L-AS1 0 0 0 0 0 0
## LURAP1L 2 1 5 2 2 1
## TTC39B 103 132 61 152 74 161
## IFNA1 0 0 0 0 0 0
## TEK 1 3 9 4 37 56
## TRBV20OR9-2 0 0 0 0 0 0
## TOMM5 193 141 72 239 164 248
## ANXA1 7419 5235 843 8028 4641 7586
## ERP44 1409 819 289 1247 1243 1349
## ZNF483 22 29 8 28 11 41
## TNFSF15 5 5 0 0 6 14
## TLR4 5614 5603 783 2237 9913 4835
## PTGS1 939 573 3239 833 493 762
## HSPA5 5573 2254 1314 6184 4272 4604
## FNBP1 3044 2688 623 3384 3172 3297
## CARD9 202 122 61 90 117 232
## TRAF2 93 84 61 122 73 147
## CLIC3 117 118 109 249 59 101
## IL2RA 72 77 22 135 68 156
## GATA3 239 259 163 423 115 331
## VIM 23313 12039 3940 13546 12311 14938
## CREM 131 82 54 264 119 132
## DKK1 0 0 0 0 0 0
## MBL2 0 0 0 0 0 0
## SAR1A 843 570 259 812 679 761
## PRF1 1981 2379 792 2768 1045 2683
## ZMIZ1 3077 1618 246 2816 1962 2313
## IFIT3 2746 2291 6447 4647 5511 4067
## TALDO1 9697 5238 4282 6621 8968 6688
## IGF2 0 0 0 0 0 1
## INS-IGF2 0 0 0 0 0 1
## IGF2-AS 0 0 0 0 0 0
## INS 0 0 0 0 0 0
## STIM1 1414 968 297 1395 1041 1524
## TRIM22 1681 1966 1748 1834 3465 2351
## PTH 0 0 0 0 0 0
## SAA1 1 0 0 1 0 0
## SLC1A2 0 0 0 1 2 2
## FOSL1 62 2 14 26 38 33
## CCND1 6 2 7 8 5 16
## JRKL 57 85 14 66 47 107
## MMP7 0 0 0 0 0 1
## MMP1 1 0 8 3 0 5
## MMP3 0 0 0 0 0 0
## CASP1 2367 1827 738 2277 3074 2575
## DLAT 151 129 18 176 112 185
## IL18 71 62 17 100 103 104
## CD3E 2819 1766 824 3676 1899 3300
## MCAM 304 141 59 260 215 295
## WNK1 4625 3194 410 3440 3652 4197
## TNFRSF1A 3632 2257 1517 2342 3439 2770
## GAPDH 22309 12305 6967 19306 18374 16707
## CD4 4230 3274 269 3684 2317 4749
## SLC2A3 11014 3382 1782 9105 8997 7950
## CLEC4D 435 271 131 301 553 236
## KLRB1 550 698 389 1631 804 866
## CD69 3042 476 88 2347 1463 1541
## CLEC2B 1639 879 743 1632 1636 1478
## OLR1 19 3 3 2 7 3
## ABCD2 148 98 24 126 87 224
## LRRK2 8698 5774 619 5202 13389 8035
## VDR 390 335 168 223 411 273
## TMBIM6 13794 8482 2915 10519 12183 12958
## PFDN5 3136 2079 1764 4056 2415 3581
## SP7 0 0 0 1 0 0
## MUCL1 0 1 0 1 0 0
## CD63 3013 1399 1483 2935 3086 2670
## SUOX 969 730 400 873 1051 1030
## RPS26 3009 2119 452 980 2354 3962
## RPL41 6491 4313 3334 10846 5686 7787
## IL23A 26 25 13 67 14 34
## DDIT3 654 136 335 544 455 462
## IFNG 212 8 2 65 15 49
## IL22 0 0 0 0 0 0
## LYZ 130738 73441 4865 53788 93617 107609
## CAPS2 3 2 0 5 0 7
## SYT1 1 9 0 2 8 2
## BTG1 10617 6644 3200 15515 11476 9724
## HCAR3 2701 587 297 1016 1825 1954
## GJB2 2 0 0 1 1 6
## GJB6 24 5 2 37 14 17
## TNFSF11 1 5 0 9 4 5
## TPT1 46600 32893 13786 70299 42053 55402
## LMO7 36 55 12 58 49 121
## TNFSF13B 1835 1589 1037 1533 1911 1457
## LAMP1 2936 2075 921 2711 2577 3059
## PSME2 1100 742 546 1581 874 1342
## GZMB 1063 889 366 2181 421 1456
## RPL36AL 1920 1216 988 2688 1928 2454
## PYGL 6179 3074 818 2730 6452 3471
## HIF1A 2410 1339 220 3644 2182 2038
## FOS 95888 25470 8105 81337 56248 35824
## JDP2 727 623 256 781 1995 582
## NOXRED1 14 3 1 6 13 11
## SERPINA1 24380 14432 6031 21178 29357 18263
## CDC42BPB 261 261 51 269 197 342
## PLA2G4D 0 0 0 0 0 0
## TRIM69 10 9 5 8 7 16
## SLC51B 0 0 0 0 0 0
## SMAD3 608 405 127 760 436 723
## CYP1A1 0 3 0 1 3 2
## AKAP13 4685 3605 698 5557 5751 5524
## MEFV 2669 2050 524 1807 2690 2051
## SOCS1 62 88 72 143 134 78
## ATXN2L 1755 1370 226 2205 1175 2023
## CD19 91 67 101 143 102 152
## ITGAL 7207 4609 1345 5246 4335 6785
## ITGAM 5657 3947 1250 4634 6765 4786
## ITGAX 5837 2110 973 3472 4553 5018
## DNAJA2 570 521 196 576 571 587
## SIAH1 107 100 61 127 84 131
## ADCY7 2805 2192 221 2582 2682 3312
## NOD2 573 525 85 369 716 854
## CMTM2 2426 1375 784 1717 3055 1515
## SF3B3 795 614 210 767 593 1087
## PSMD7 689 441 222 742 546 736
## WWOX 51 33 12 72 37 71
## MAF 409 318 139 534 269 730
## SLC7A5 242 116 77 473 169 270
## CXCL16 2695 1444 287 2520 2554 2152
## XAF1 579 629 861 675 777 1130
## CD68 4295 3277 662 3756 3311 4436
## PER1 771 1199 209 1757 2710 867
## NOS2 0 0 0 0 0 5
## TRAF4 103 30 26 189 43 127
## CCL2 10 2 4 3 6 34
## CCL5 7086 3003 4154 5103 2301 5364
## CCL3 414 124 185 309 151 175
## CCR7 275 663 368 864 528 829
## STAT3 4095 3399 1343 3514 4747 4148
## SOST 0 0 2 0 0 0
## ITGA2B 695 313 4211 478 232 507
## EFCAB13 19 13 1 30 19 30
## NPEPPS 836 662 155 605 769 819
## TBX21 472 261 161 509 147 483
## COL1A1 0 0 0 1 1 1
## MRPS23 116 139 52 131 84 148
## MIR21 3 3 0 4 3 2
## RPS6KB1 297 260 78 336 295 407
## ACE 44 29 11 66 24 63
## ERN1 1195 1166 164 1304 1369 1573
## PRTN3 2 5 55 3 24 3
## PLIN5 114 48 112 42 130 67
## RETN 154 20 113 51 46 12
## CCL25 0 0 2 1 1 0
## ICAM1 2216 525 216 1817 1109 1429
## TYK2 1661 1332 689 1085 1610 1585
## SMARCA4 640 538 226 764 484 777
## ACP5 204 321 122 221 253 243
## JUNB 37990 6947 6873 53240 26993 20662
## CYP4F22 58 108 13 128 9 190
## JAK3 1939 809 2470 1236 1292 1598
## JUND 15330 2439 5796 14165 6179 6224
## CEBPA 1153 425 251 828 586 878
## CEBPG 264 227 68 239 182 306
## ACP7 1 0 0 3 0 0
## ZFP36 42723 5930 3802 32192 18942 14652
## TGFB1 6378 2836 3288 6006 4778 4219
## RPS19 8530 6537 7662 14764 6639 11260
## PSG2 0 0 0 0 0 0
## FUT2 2 1 8 2 0 3
## NKG7 6852 2477 1843 6202 2157 4537
## ZNF415 7 3 0 3 9 8
## LILRB2 4463 3291 560 4059 3902 4231
## LILRA5 2083 1808 1877 1674 2110 1530
## KIR3DL1 39 190 11 257 90 57
## KIR3DL2 25 24 10 192 7 27
## SMOX 114 62 704 139 104 61
## BMP2 4 2 1 5 4 5
## GINS1 5 3 3 3 7 11
## PLCG1 543 547 188 768 471 971
## YWHAB 5638 3557 1687 4444 5084 5949
## PI3 1511 360 287 227 1136 343
## MMP9 3975 1320 1169 1820 3970 1322
## CD40 136 115 84 199 125 201
## PFDN4 44 34 23 53 32 55
## BMP7 0 0 0 0 0 0
## RPS21 3578 2692 1913 7142 3424 4665
## MX1 883 981 2820 760 949 1712
## PFKL 1204 854 355 1231 773 1309
## IL17RA 5961 4926 1413 4540 7707 4768
## UBE2L3 980 705 515 908 848 1010
## TPST2 1823 819 814 1383 1019 1244
## XBP1 839 677 365 1284 652 817
## UQCR10 464 347 254 617 426 559
## SEC14L2 11 21 8 39 19 29
## APOL6 1119 1083 810 1719 1373 1655
## APOL1 541 461 297 673 554 652
## TYMP 4321 1627 3882 3045 3062 3786
## BEND2 68 43 333 84 12 54
## PHEX 15 5 2 25 5 14
## TIMP1 1750 1385 1211 1516 2170 1174
## FOXP3 57 45 35 81 44 69
## MSN 28636 17459 4505 21074 25441 23087
## PGK1 8436 4369 1012 6732 7015 7442
## LAMP2 6862 4517 786 5205 8214 5884
## CD40LG 76 131 38 187 73 183
## IRAK1 1696 801 279 1916 1314 1719
## COX2 53689 34513 224597 85345 37834 46152
## GSM3308461 GSM3308462 GSM3308463 GSM3308464 GSM3308465 GSM3308466
## TNFRSF9 140 177 71 122 224 283
## ENO1 5089 6984 5744 6257 7165 6578
## PIK3CD 8324 7112 6609 7134 5200 8675
## PGD 5458 6080 4757 5740 4419 8786
## MTHFR 456 494 454 314 360 409
## TNFRSF1B 13075 16553 16909 14482 12367 15082
## PINK1 970 936 732 957 629 1066
## IFNLR1 45 98 47 59 77 49
## RUNX3 3460 2879 4128 3907 3621 2662
## SH3BGRL3 8650 10044 11673 12686 12570 13369
## CD52 2989 4093 3331 4484 5161 2625
## IFI6 510 5623 5129 3634 2373 1325
## ZC3H12A 491 311 508 557 530 1184
## UTP11 71 134 86 87 69 74
## JUN 10163 5429 1370 10743 18149 7780
## KANK4 0 0 0 1 0 0
## EFCAB7 31 40 25 24 16 14
## IL23R 0 0 1 11 5 1
## ADGRL2 0 0 0 0 0 0
## GBP3 239 195 172 137 265 303
## GBP1 677 1511 1441 882 854 1907
## GBP5 2172 3657 3029 2553 2550 4707
## TGFBR3 643 430 1403 841 865 573
## VCAM1 2 4 2 2 4 6
## PTPN22 331 524 447 380 303 277
## CD160 163 46 164 145 200 41
## FCGR1A 522 535 563 599 840 1719
## MCL1 27351 19651 20489 24814 21244 39068
## CTSK 69 29 52 32 40 55
## RORC 36 42 54 54 46 7
## S100A9 142511 116253 102066 163151 119400 217249
## S100A12 6976 3409 2818 5461 3283 9373
## S100A8 51105 38493 38190 62082 46546 85549
## IL6R 5292 5108 4758 5307 3512 5400
## RIT1 1509 1357 1312 1400 1198 1872
## BGLAP 5 4 9 7 5 7
## IFI16 2325 5326 5494 4036 2443 3805
## AIM2 197 164 155 170 190 324
## CRP 0 0 0 0 0 0
## FCGR2A 15816 14311 16678 18568 12047 16618
## HSPA6 1882 2213 2920 2333 1430 2086
## FCGR3A 19242 21704 26233 25078 14703 23559
## SELL 46154 38917 41920 49800 33623 51861
## GLUL 15195 14101 15830 17034 11108 23426
## PTGS2 13720 11508 2975 17731 10594 29561
## CRB1 2 1 1 0 0 1
## KDM5B 478 486 552 432 356 551
## IL10 2 0 4 0 7 2
## YOD1 262 167 291 172 220 226
## HHAT 39 43 23 31 30 13
## TRAF5 359 310 373 240 316 171
## NLRP3 893 991 804 871 917 1343
## LINC01250 0 0 0 0 1 0
## RPS7 7439 7389 7128 7937 9624 5068
## RSAD2 137 4156 6957 2162 1698 649
## FOSL2 4388 3971 3032 3264 3485 7253
## REL 1133 1334 1381 844 839 1092
## TGFA 681 522 464 572 362 818
## DYSF 7081 4859 5268 6676 4740 10257
## HK2 1115 1486 1041 892 973 2163
## CD8A 1367 1103 1202 1797 2451 996
## CD8B 788 534 522 888 1121 243
## EIF5B 499 479 481 409 496 377
## IL1R1 331 223 232 219 196 252
## RGPD6 63 74 83 46 62 56
## IL1A 0 0 1 0 1 9
## IL1B 604 760 550 1502 882 4056
## IL37 0 0 0 0 0 0
## IL36RN 0 0 0 0 0 0
## IL1F10 0 0 0 0 0 0
## IL1RN 3099 3043 4435 4639 4784 7994
## NMI 1444 1770 2488 1851 1213 2389
## TNFAIP6 287 828 792 1239 599 1343
## IFIH1 343 811 928 530 503 598
## SCN1A 0 0 0 0 0 0
## ABCB11 0 3 0 0 0 3
## RBM45 48 42 56 60 56 41
## FRZB 1 0 0 0 0 0
## TFPI 5 2 11 5 6 3
## STAT1 2977 6063 5807 4432 4415 6631
## NABP1 722 638 607 704 571 1114
## SF3B1 4802 4494 4796 4180 3647 4949
## CASP10 283 416 395 238 270 339
## CD28 621 521 615 475 607 349
## CTLA4 47 60 63 74 60 56
## ICOS 179 104 168 182 171 145
## NDUFS1 444 533 635 473 390 475
## CXCR2 20634 23466 29481 29974 13890 22692
## IRS1 55 132 68 106 144 32
## CCL20 1 0 1 1 5 5
## ATG16L1 283 258 298 208 242 208
## GPR35 71 148 83 75 119 65
## PDCD1 41 36 26 34 34 41
## PPARG 1 2 3 2 6 1
## RPL15 12035 12743 12111 12877 15168 8044
## EOMES 93 79 183 134 122 136
## CX3CR1 871 1840 2175 1014 1143 1945
## ACKR2 0 0 0 0 2 1
## CCR2 465 1785 847 550 434 536
## CCRL2 25 50 43 36 35 59
## TLR9 66 113 69 65 43 56
## ARHGEF3 1131 940 1478 869 1176 1000
## ADAMTS9 0 0 0 0 1 0
## TMEM45A 1 8 2 2 0 0
## CD80 4 13 6 4 8 1
## CD86 601 1511 777 741 697 713
## MIX23 21 27 25 25 23 19
## PLS1 17 6 22 21 14 9
## PTX3 57 55 41 49 83 138
## GOLIM4 62 139 72 49 60 67
## MYNN 276 348 343 294 261 436
## TNFSF10 2985 5450 5035 4840 2499 4249
## ADIPOQ 0 0 0 0 0 0
## SPON2 366 479 843 322 482 596
## S100P 4714 2668 1468 2655 3876 918
## WDR1 5752 6360 6675 6188 5467 6309
## CD38 208 347 270 190 252 352
## PPARGC1A 4 4 1 3 2 3
## TMPRSS11B 0 0 0 0 0 0
## CSN3 0 0 0 0 0 0
## ALB 0 0 1 0 0 0
## CXCL8 29532 30376 17855 42655 65930 108930
## CXCL2 10 18 8 27 22 63
## AREG 23 64 7 29 30 147
## CXCL10 9 22 31 22 34 37
## CXCL13 1 3 1 2 0 2
## SPP1 62 33 79 18 28 56
## HERC6 155 391 527 241 322 168
## NFKB1 935 897 1077 775 751 1057
## SEC24B 478 498 560 341 386 406
## EGF 9 14 113 41 55 8
## IL2 0 2 1 3 1 1
## IL21 1 2 1 0 2 4
## IL21-AS1 3 1 2 3 5 3
## SLC7A11 15 9 20 9 9 16
## IL15 89 116 71 72 70 89
## EDNRA 0 1 0 0 0 0
## TLR2 4074 3214 3934 4324 3494 4797
## FGB 0 0 0 0 0 0
## DDX60 213 988 1390 564 663 390
## SPCS3 1799 2380 1994 1742 1755 1959
## TLR3 10 5 23 5 12 8
## OSMR 42 30 53 35 21 30
## GZMK 628 183 668 682 819 609
## GZMA 1071 524 1764 1658 1634 1265
## ANKRD55 105 42 70 63 58 81
## CENPK 66 66 119 22 26 18
## CAST 2363 2880 3623 2171 2336 2968
## ERAP1 1272 2283 2036 1272 1403 1144
## ERAP2 1428 159 1788 2629 142 1322
## TNFAIP8 1336 1397 1717 1158 1175 1069
## CSF2 0 0 0 0 0 0
## IL5 0 2 0 1 0 0
## IL13 0 0 0 0 0 0
## IL4 1 3 3 4 4 4
## CD14 5164 12149 7434 9002 7667 11681
## CSNK1A1 1557 1885 1708 1523 1354 1762
## PPARGC1B 122 121 99 99 132 129
## TNIP1 4789 4850 5449 5916 4080 6197
## ATOX1 153 185 206 184 177 202
## FAXDC2 101 137 284 149 208 96
## IL12B 1 2 1 0 1 0
## MIR146A 0 1 0 0 1 0
## PDLIM7 1870 1491 1601 2154 1379 2026
## SERPINB1 4574 4671 4664 5455 5317 5693
## SSR1 1812 2886 2371 2194 2325 2418
## CD83 329 418 468 385 630 1316
## SOX4 139 160 82 144 181 134
## CMAHP 54 100 102 38 62 66
## HLA-A 43706 53402 52797 44242 42077 45235
## HLA-C 90906 63703 106014 119261 83981 109743
## HLA-B 95532 114541 119279 116613 127056 137452
## MICA 125 173 129 124 101 109
## LTA 70 47 69 48 59 35
## TNF 149 144 221 308 315 387
## HLA-DRB1 1594 6786 3063 4529 7066 3605
## HLA-DQB1 178 1543 199 1102 1038 869
## PPARD 298 337 562 239 224 188
## CCND3 3873 4378 3973 4737 4659 5193
## VEGFA 133 216 109 143 226 169
## RUNX2 459 502 607 438 402 443
## IL17A 0 0 0 0 0 0
## IL17F 0 0 0 0 0 0
## PRDM1 505 535 829 630 511 579
## ATG5 291 431 408 323 346 360
## TRAF3IP2 230 234 223 191 210 117
## NCOA7 304 508 454 372 280 295
## SGK1 2867 3922 3148 2991 3074 3603
## IFNGR1 2525 3567 3303 3161 1966 2862
## TNFAIP3 3845 1630 2595 4641 6592 14267
## SOD2 46281 39191 44622 55227 39884 84406
## LPAL2 14 6 18 10 3 25
## PLG 0 0 0 1 0 1
## CCR6 59 94 103 72 63 33
## RAC1 2632 3550 3438 3085 2628 2832
## ZNF316 798 730 663 567 647 776
## AHR 509 830 901 490 595 1445
## IL6 8 3 4 4 3 2
## TOMM7 2160 1819 2136 2147 2677 1232
## CYCS 512 587 517 593 804 727
## AQP1 3 1 5 0 3 0
## NT5C3A 740 978 1366 936 784 879
## EGFR 0 0 0 0 0 0
## CD36 1642 3186 1889 1531 2287 2292
## SAMD9 1393 3848 3775 2341 1566 2509
## SERPINE1 5 4 18 9 11 6
## CUX1 1466 1781 1486 1565 1603 2035
## PSMC2 258 436 347 312 311 293
## NAMPT 48235 39070 53261 58323 38779 85285
## HYAL4 0 0 0 0 0 0
## LEP 5 17 8 8 9 1
## CALD1 4 8 44 13 9 10
## BRAF 847 697 773 627 654 857
## EZH2 72 73 66 43 60 64
## DNAJB6 1321 1690 1647 1676 1311 1574
## CSMD1 15 28 2 1 0 16
## CTSB 3766 7076 4885 5627 4323 5330
## EGR3 175 638 466 1068 312 1567
## TNFRSF10A 176 131 148 111 124 90
## BNIP3L 1860 2839 2577 2406 1808 2535
## DUSP4 32 40 64 103 89 85
## NRG1 43 217 166 70 133 86
## RPL7 9166 8251 9163 8838 10838 5586
## IL7 8 25 18 13 20 12
## GEM 0 1 0 0 3 3
## MYC 738 639 864 699 543 233
## GPT 4 4 4 1 0 0
## JAK2 1215 1116 939 957 971 1575
## CD274 132 197 220 223 192 372
## IL33 0 0 0 0 0 1
## LURAP1L-AS1 0 0 0 0 0 0
## LURAP1L 0 0 2 3 2 0
## TTC39B 164 126 197 112 168 93
## IFNA1 0 0 0 0 0 0
## TEK 39 5 5 56 12 14
## TRBV20OR9-2 0 0 0 0 0 0
## TOMM5 193 212 205 232 247 183
## ANXA1 4659 6611 6981 5716 5523 7445
## ERP44 1134 1399 1367 1514 1455 1650
## ZNF483 43 18 38 15 32 21
## TNFSF15 4 1 1 5 4 5
## TLR4 7292 8273 7395 7251 4769 8115
## PTGS1 369 636 1418 781 952 504
## HSPA5 5762 5049 4719 6105 5915 6458
## FNBP1 3427 3571 4004 3577 2769 3456
## CARD9 154 238 120 86 125 118
## TRAF2 116 118 145 97 97 82
## CLIC3 103 98 169 110 103 87
## IL2RA 160 100 150 124 78 56
## GATA3 325 230 391 336 257 170
## VIM 16150 15884 17298 16297 14501 17763
## CREM 131 127 135 143 119 184
## DKK1 0 0 0 0 0 0
## MBL2 0 0 0 0 0 0
## SAR1A 614 760 978 740 695 937
## PRF1 1607 2901 5745 2039 1981 3408
## ZMIZ1 1973 3181 2626 2203 1656 2265
## IFIT3 2011 15323 17354 10871 9124 6621
## TALDO1 8799 9541 9408 12494 9027 10803
## IGF2 0 0 1 0 0 0
## INS-IGF2 0 0 1 0 0 0
## IGF2-AS 0 0 0 0 0 0
## INS 0 0 0 0 0 0
## STIM1 1378 1405 1814 1358 1201 1260
## TRIM22 1627 4296 4690 3118 2723 4144
## PTH 0 0 0 0 0 0
## SAA1 1 0 0 0 1 1
## SLC1A2 3 0 1 3 1 2
## FOSL1 20 16 17 55 31 142
## CCND1 6 7 13 7 4 3
## JRKL 100 85 91 79 56 49
## MMP7 0 0 0 0 0 0
## MMP1 0 0 8 1 1 0
## MMP3 0 0 0 0 0 0
## CASP1 2493 3090 2896 3409 2788 4338
## DLAT 172 237 195 163 172 139
## IL18 61 172 65 71 82 89
## CD3E 3417 1947 3148 3752 3952 1784
## MCAM 275 241 206 193 237 359
## WNK1 4575 4708 5035 4263 3358 4387
## TNFRSF1A 3640 4603 4725 4369 2730 4192
## GAPDH 15937 18868 15523 18561 18010 22887
## CD4 3390 5549 3737 4241 3717 3373
## SLC2A3 15074 6959 7787 10942 9408 18154
## CLEC4D 621 506 312 566 294 1082
## KLRB1 761 373 1289 1155 837 523
## CD69 1789 785 702 1354 3108 3060
## CLEC2B 1778 1468 1921 2152 1602 2817
## OLR1 21 3 15 7 10 11
## ABCD2 157 125 187 136 194 109
## LRRK2 9292 7817 9374 9783 6317 15071
## VDR 355 492 600 357 352 515
## TMBIM6 12559 15317 15040 16106 13010 15152
## PFDN5 2659 3130 3040 3265 3759 2423
## SP7 0 1 0 1 0 0
## MUCL1 1 0 0 0 0 1
## CD63 2732 2655 2550 3308 2974 3647
## SUOX 974 1145 1180 1118 874 1304
## RPS26 596 4880 708 783 898 682
## RPL41 6345 6451 7071 7875 8965 4400
## IL23A 39 25 38 29 41 27
## DDIT3 728 401 372 478 350 791
## IFNG 39 15 34 39 131 82
## IL22 0 0 0 1 0 0
## LYZ 80492 125208 52500 49393 77717 37750
## CAPS2 6 3 5 8 4 4
## SYT1 4 7 1 1 7 5
## BTG1 10233 9433 8074 10181 10475 11260
## HCAR3 3405 1381 3599 3602 3877 5767
## GJB2 1 4 0 0 1 6
## GJB6 39 13 4 18 34 71
## TNFSF11 4 0 1 2 1 0
## TPT1 51861 47618 50317 53125 60695 38202
## LMO7 91 59 73 62 52 32
## TNFSF13B 2458 3515 3603 3824 2611 3207
## LAMP1 2867 3028 2869 3063 2937 3229
## PSME2 934 1576 1427 1137 1548 1587
## GZMB 686 1046 1456 1050 946 1634
## RPL36AL 1898 2177 1902 2335 2757 1791
## PYGL 7717 4631 4976 6689 4655 11724
## HIF1A 1973 2465 2872 2051 1920 3886
## FOS 48833 52199 10706 71840 100052 56916
## JDP2 656 977 726 634 552 875
## NOXRED1 8 6 11 6 8 13
## SERPINA1 26150 26330 27619 31625 23412 36921
## CDC42BPB 186 331 223 172 139 184
## PLA2G4D 0 0 0 0 0 0
## TRIM69 7 31 14 11 19 16
## SLC51B 0 0 0 0 0 0
## SMAD3 570 613 720 558 565 339
## CYP1A1 0 2 2 0 0 1
## AKAP13 4547 5519 5141 3840 3688 6212
## MEFV 3084 3834 3427 3236 1924 3422
## SOCS1 64 54 58 86 68 118
## ATXN2L 1998 1787 1861 1760 1702 1501
## CD19 96 290 161 89 114 71
## ITGAL 5208 5155 6623 5841 5488 5761
## ITGAM 6329 5457 4940 6177 4591 8012
## ITGAX 5866 4514 5066 5176 4128 7309
## DNAJA2 650 724 581 597 531 652
## SIAH1 120 150 136 90 109 116
## ADCY7 2902 3249 2929 2285 2040 2520
## NOD2 403 679 1544 380 962 711
## CMTM2 2563 1802 1789 3614 2690 3580
## SF3B3 808 906 1031 799 880 752
## PSMD7 521 726 682 605 656 706
## WWOX 31 35 36 43 45 28
## MAF 424 405 551 414 478 420
## SLC7A5 172 307 170 412 214 209
## CXCL16 1514 2664 1569 2282 1631 3460
## XAF1 647 2287 2794 1414 1283 1056
## CD68 2483 5852 3188 3409 4021 3221
## PER1 385 435 443 469 467 763
## NOS2 0 0 1 0 0 0
## TRAF4 82 147 85 104 78 70
## CCL2 6 154 22 59 18 25
## CCL5 3250 1922 5942 5491 6940 3846
## CCL3 254 504 120 323 347 892
## CCR7 840 722 790 637 544 231
## STAT3 4894 5638 5620 4961 3646 6563
## SOST 0 0 0 0 0 1
## ITGA2B 173 162 1421 589 517 278
## EFCAB13 9 23 30 10 20 14
## NPEPPS 1035 1029 937 847 698 1225
## TBX21 319 270 655 374 358 354
## COL1A1 0 0 0 0 0 0
## MRPS23 116 191 173 144 139 121
## MIR21 3 5 7 9 3 5
## RPS6KB1 382 388 441 313 329 284
## ACE 59 36 41 47 31 9
## ERN1 1304 1030 1489 1164 889 1219
## PRTN3 5 8 2 4 0 6
## PLIN5 117 112 77 138 70 132
## RETN 54 44 216 34 79 48
## CCL25 0 0 1 0 0 0
## ICAM1 1395 1502 1417 2121 1894 3540
## TYK2 1701 2061 1793 1583 1214 1929
## SMARCA4 685 656 699 623 605 480
## ACP5 186 672 259 389 382 200
## JUNB 37761 26337 18348 49774 37584 32016
## CYP4F22 49 9 42 43 36 60
## JAK3 2206 1410 1986 1495 1534 2931
## JUND 7376 6399 3688 7954 9481 8295
## CEBPA 752 949 559 674 756 876
## CEBPG 205 313 269 219 220 227
## ACP7 0 0 1 0 0 0
## ZFP36 22787 16942 10164 35867 36470 45945
## TGFB1 4805 4746 5724 5347 4435 5166
## RPS19 9117 8323 9109 8901 10456 5975
## PSG2 0 0 0 0 0 0
## FUT2 3 1 2 3 1 5
## NKG7 3087 2522 6181 5237 7096 4322
## ZNF415 7 7 26 5 3 3
## LILRB2 3877 5147 3993 4556 3699 4783
## LILRA5 2796 3628 2321 2847 2289 3573
## KIR3DL1 42 51 140 57 90 9
## KIR3DL2 30 54 120 28 14 10
## SMOX 46 65 280 129 147 53
## BMP2 22 4 18 8 5 5
## GINS1 7 8 14 5 14 8
## PLCG1 881 609 791 652 633 412
## YWHAB 5375 6365 5940 5737 5895 7457
## PI3 1183 1524 1933 1073 1586 2898
## MMP9 3789 1613 1226 1445 1745 6318
## CD40 125 261 149 103 126 83
## PFDN4 35 44 65 43 49 47
## BMP7 0 0 0 0 0 0
## RPS21 4186 3712 3981 4165 5521 2488
## MX1 544 6305 7286 4480 3169 1695
## PFKL 1003 1370 1097 1022 962 887
## IL17RA 6657 6493 5748 6354 4610 8184
## UBE2L3 903 1132 1160 1059 970 1068
## TPST2 1102 895 1434 1353 1321 1149
## XBP1 743 1212 1094 978 804 917
## UQCR10 426 577 527 613 613 499
## SEC14L2 66 35 26 22 30 15
## APOL6 1262 2096 2568 1399 1465 2340
## APOL1 537 810 804 899 784 999
## TYMP 2958 6644 3796 4225 4051 3399
## BEND2 15 12 110 35 97 15
## PHEX 7 4 8 5 15 15
## TIMP1 1504 1526 1424 1531 1250 1827
## FOXP3 84 89 67 98 94 66
## MSN 23913 24737 27901 29904 26490 29191
## PGK1 7390 7707 6845 8455 8412 9688
## LAMP2 7222 7687 7571 8039 5767 8886
## CD40LG 163 99 191 194 109 46
## IRAK1 1310 1523 1251 1267 1382 1416
## COX2 41656 51261 45220 47337 62463 35140
## GSM3308467 GSM3308468 GSM3308469 GSM3308470 GSM3308471 GSM3308472
## TNFRSF9 126 117 153 120 117 95
## ENO1 6828 3846 4229 7213 6318 5957
## PIK3CD 5447 5877 5368 6406 5104 3327
## PGD 4514 4103 4968 5792 5069 3192
## MTHFR 552 347 523 373 511 367
## TNFRSF1B 12429 11876 13734 12283 13535 11435
## PINK1 580 577 843 746 586 528
## IFNLR1 86 55 28 25 59 73
## RUNX3 4682 2618 4416 3269 2866 10497
## SH3BGRL3 10737 8976 9497 13765 9429 9835
## CD52 5033 2097 2376 3994 3097 5247
## IFI6 6406 4578 1032 370 1711 763
## ZC3H12A 501 1468 1409 3438 718 660
## UTP11 112 32 43 59 56 67
## JUN 7397 23010 43554 12353 25317 32756
## KANK4 0 0 0 0 0 0
## EFCAB7 24 8 17 10 12 23
## IL23R 1 0 0 0 2 3
## ADGRL2 0 0 0 0 0 0
## GBP3 461 191 202 130 224 131
## GBP1 1780 1604 959 201 1642 365
## GBP5 3139 5383 3454 1068 5623 1603
## TGFBR3 1231 596 681 470 624 1605
## VCAM1 5 0 9 12 0 11
## PTPN22 519 201 293 228 257 371
## CD160 298 90 120 62 81 139
## FCGR1A 1061 1626 849 581 1652 307
## MCL1 22516 43784 54334 32861 27603 20207
## CTSK 78 56 105 85 93 32
## RORC 42 18 37 15 19 46
## S100A9 124763 155767 128974 225091 105031 59677
## S100A12 4436 5269 5015 6801 4394 1241
## S100A8 44018 62735 51139 89867 45173 20690
## IL6R 3441 3229 3385 3095 3591 1996
## RIT1 1165 2008 1532 1896 1192 940
## BGLAP 7 11 4 10 6 6
## IFI16 4242 1838 1333 907 1869 1055
## AIM2 143 138 102 66 164 47
## CRP 0 0 0 0 0 0
## FCGR2A 10671 11862 9917 11013 10986 5285
## HSPA6 1357 1536 1205 1277 1299 610
## FCGR3A 19021 18009 14137 8487 18251 10677
## SELL 35711 31871 41725 27774 30148 17656
## GLUL 14050 18911 14725 13028 13269 9963
## PTGS2 14882 17881 14396 6529 8739 2923
## CRB1 1 1 0 1 1 0
## KDM5B 423 610 799 583 442 351
## IL10 12 8 7 16 4 6
## YOD1 172 187 370 354 212 179
## HHAT 55 32 22 35 31 65
## TRAF5 353 196 246 211 285 316
## NLRP3 1070 821 1081 1018 1447 1083
## LINC01250 0 0 0 0 0 0
## RPS7 9329 4948 6277 10473 8128 10458
## RSAD2 7504 3927 342 56 934 132
## FOSL2 3340 7776 5537 5180 4065 8138
## REL 1094 1049 1292 1048 1163 1141
## TGFA 331 572 410 464 403 202
## DYSF 4253 7096 5394 4949 5263 2152
## HK2 975 1112 1451 1034 1337 562
## CD8A 3735 1125 623 1520 1004 5363
## CD8B 1502 554 416 1334 368 1656
## EIF5B 589 290 336 353 487 473
## IL1R1 184 377 479 400 217 190
## RGPD6 67 61 83 66 58 85
## IL1A 3 8 13 9 2 2
## IL1B 2823 2209 2437 3780 1797 363
## IL37 0 0 0 0 0 0
## IL36RN 0 0 0 0 0 0
## IL1F10 0 0 0 0 0 0
## IL1RN 4112 10007 5963 16721 3984 1005
## NMI 1706 967 922 977 997 602
## TNFAIP6 801 637 569 273 1143 247
## IFIH1 825 697 509 313 582 246
## SCN1A 0 0 0 0 0 0
## ABCB11 0 1 3 1 2 0
## RBM45 63 23 28 37 42 50
## FRZB 0 0 0 0 0 0
## TFPI 11 1 5 5 1 4
## STAT1 6817 4126 3793 1848 5392 1926
## NABP1 512 1110 1394 475 966 330
## SF3B1 4249 4165 4757 4240 4020 3500
## CASP10 374 224 374 223 427 334
## CD28 723 501 541 792 431 564
## CTLA4 94 58 63 70 66 66
## ICOS 263 294 112 358 146 201
## NDUFS1 674 246 289 323 353 363
## CXCR2 13559 11526 17491 8640 10358 7005
## IRS1 192 75 74 46 66 41
## CCL20 1 6 18 12 0 6
## ATG16L1 286 251 282 300 309 383
## GPR35 79 85 94 129 98 99
## PDCD1 90 24 33 49 21 91
## PPARG 9 4 5 13 4 1
## RPL15 15294 7584 10617 16786 13302 15961
## EOMES 296 49 121 93 74 209
## CX3CR1 2673 286 462 391 1563 365
## ACKR2 1 4 0 0 0 0
## CCR2 933 124 351 441 540 128
## CCRL2 74 35 37 50 72 28
## TLR9 57 51 91 68 51 38
## ARHGEF3 1605 923 1227 1009 1157 1012
## ADAMTS9 0 0 0 0 0 0
## TMEM45A 1 1 0 1 0 3
## CD80 14 7 3 3 7 9
## CD86 935 354 532 516 1025 1119
## MIX23 25 7 16 15 19 29
## PLS1 10 11 23 9 8 17
## PTX3 62 92 141 216 206 45
## GOLIM4 86 28 69 35 81 69
## MYNN 323 338 406 330 360 318
## TNFSF10 4724 2223 1561 1607 2136 606
## ADIPOQ 0 0 0 0 0 0
## SPON2 1159 464 984 141 435 2010
## S100P 2783 4807 4862 7023 1814 2013
## WDR1 6270 3755 3829 4551 4689 4929
## CD38 395 179 181 101 209 324
## PPARGC1A 1 3 10 2 0 6
## TMPRSS11B 0 0 2 0 0 0
## CSN3 0 0 0 0 0 0
## ALB 1 0 0 0 0 0
## CXCL8 31577 142856 229948 93583 82191 24395
## CXCL2 65 81 82 103 40 14
## AREG 38 133 2145 822 195 695
## CXCL10 60 17 12 3 52 11
## CXCL13 7 0 1 0 0 1
## SPP1 53 16 45 58 83 32
## HERC6 572 280 107 100 162 136
## NFKB1 902 741 849 906 892 683
## SEC24B 380 399 532 422 441 388
## EGF 44 24 10 101 10 18
## IL2 0 0 0 1 0 0
## IL21 3 0 1 0 2 1
## IL21-AS1 6 0 1 1 1 0
## SLC7A11 11 20 10 14 29 7
## IL15 145 34 56 49 89 72
## EDNRA 0 0 0 0 0 0
## TLR2 2998 4129 8510 5582 3308 1422
## FGB 0 0 0 0 0 0
## DDX60 1622 868 311 127 502 177
## SPCS3 2380 1058 1460 1779 1607 1490
## TLR3 22 12 13 9 10 20
## OSMR 22 42 41 31 30 14
## GZMK 835 612 546 502 434 2013
## GZMA 2446 704 894 595 865 2256
## ANKRD55 40 38 66 38 78 38
## CENPK 26 28 65 55 20 90
## CAST 2837 2059 1811 2026 2320 2845
## ERAP1 2202 638 909 745 1125 1275
## ERAP2 169 1794 279 1765 1731 1626
## TNFAIP8 1457 725 921 886 1083 819
## CSF2 1 1 0 0 0 2
## IL5 1 0 0 0 0 0
## IL13 1 1 0 1 0 2
## IL4 3 2 1 0 4 1
## CD14 10050 5701 6017 8446 8454 5375
## CSNK1A1 1807 1179 1251 1421 1431 1104
## PPARGC1B 119 61 159 107 215 77
## TNIP1 4838 5071 4161 5643 4912 3090
## ATOX1 204 117 169 192 166 203
## FAXDC2 186 110 124 273 152 155
## IL12B 0 2 2 0 0 0
## MIR146A 0 0 0 0 0 0
## PDLIM7 1117 2172 1804 1991 1349 944
## SERPINB1 4499 3646 4458 5285 4082 3184
## SSR1 2602 1477 1628 1837 1992 1740
## CD83 710 1795 1437 1554 1552 588
## SOX4 106 64 154 116 256 204
## CMAHP 99 69 83 58 90 91
## HLA-A 45640 43315 43164 43202 38993 47557
## HLA-C 74176 106002 88929 70934 61996 59129
## HLA-B 105335 121942 118300 87553 94441 88479
## MICA 146 87 137 138 190 99
## LTA 82 50 35 39 47 31
## TNF 168 193 153 251 390 219
## HLA-DRB1 4890 2982 3114 4849 7022 6455
## HLA-DQB1 2472 1392 772 3092 1525 3624
## PPARD 254 204 243 320 219 269
## CCND3 4605 3717 7781 4734 4146 5538
## VEGFA 163 221 210 348 258 317
## RUNX2 457 391 882 649 374 343
## IL17A 0 0 0 0 0 0
## IL17F 0 0 0 0 0 0
## PRDM1 1378 670 1378 2938 547 1164
## ATG5 420 259 328 370 361 394
## TRAF3IP2 157 98 202 175 144 162
## NCOA7 937 272 373 307 302 276
## SGK1 5463 4446 2614 3517 3823 1232
## IFNGR1 2074 1632 2872 2244 2279 1379
## TNFAIP3 3579 22245 42595 53001 10065 14273
## SOD2 31081 43768 41442 40803 50478 22592
## LPAL2 21 7 23 10 10 28
## PLG 1 0 2 0 0 1
## CCR6 83 48 81 35 58 133
## RAC1 2856 1718 1633 3039 2499 1952
## ZNF316 590 883 684 1400 567 681
## AHR 1047 948 1890 1170 1833 768
## IL6 1 21 7 6 19 4
## TOMM7 1764 1382 1810 2897 2494 2827
## CYCS 982 606 902 725 862 909
## AQP1 2 1 2 6 3 0
## NT5C3A 1107 715 509 524 694 482
## EGFR 0 0 0 0 0 0
## CD36 3067 1359 1144 2332 3281 1009
## SAMD9 3464 2321 1641 549 1731 774
## SERPINE1 14 15 17 17 19 9
## CUX1 1691 1559 1691 1903 2125 1611
## PSMC2 432 150 234 278 322 292
## NAMPT 38029 54930 52721 61809 43974 21114
## HYAL4 0 0 0 0 0 1
## LEP 2 2 3 2 2 0
## CALD1 36 5 7 32 18 13
## BRAF 658 594 798 672 657 510
## EZH2 96 47 64 39 71 68
## DNAJB6 1106 1270 1235 1579 1218 1171
## CSMD1 7 0 1 0 21 1
## CTSB 5765 2594 3671 5670 5794 4771
## EGR3 1165 1335 741 581 492 108
## TNFRSF10A 134 133 127 148 105 92
## BNIP3L 2070 1338 1498 2130 1810 1049
## DUSP4 91 146 128 75 56 291
## NRG1 158 135 56 243 204 69
## RPL7 10713 5786 7433 13099 9451 10603
## IL7 22 6 10 6 7 11
## GEM 2 4 4 0 1 3
## MYC 920 316 387 1067 281 475
## GPT 3 0 1 2 2 8
## JAK2 1112 1006 1524 1006 1247 657
## CD274 248 233 131 65 272 72
## IL33 0 0 0 0 0 0
## LURAP1L-AS1 0 0 0 0 0 0
## LURAP1L 2 2 0 1 1 2
## TTC39B 146 114 156 83 91 179
## IFNA1 0 0 0 0 0 0
## TEK 6 36 73 51 27 14
## TRBV20OR9-2 0 0 0 0 0 0
## TOMM5 261 113 141 202 203 290
## ANXA1 7536 3346 5904 7427 7518 7929
## ERP44 1416 1178 1268 1065 1460 1077
## ZNF483 44 16 32 51 20 35
## TNFSF15 16 3 6 3 9 4
## TLR4 6398 5075 6919 3098 6019 2654
## PTGS1 689 709 658 1068 724 453
## HSPA5 5605 6432 6402 5323 5157 7013
## FNBP1 3436 1943 2426 2509 2407 2703
## CARD9 195 90 142 126 192 158
## TRAF2 149 65 104 98 77 106
## CLIC3 104 56 150 37 53 366
## IL2RA 280 48 137 100 111 115
## GATA3 412 171 296 284 185 434
## VIM 16786 13791 11956 22450 14853 16144
## CREM 134 162 198 181 145 436
## DKK1 0 0 0 0 0 0
## MBL2 0 0 0 0 0 0
## SAR1A 866 716 795 963 650 641
## PRF1 5288 717 2343 525 1361 4129
## ZMIZ1 2250 2336 3080 2679 2197 1981
## IFIT3 21679 19009 3558 702 8494 1363
## TALDO1 6608 6710 7858 8515 7219 4825
## IGF2 0 0 0 0 0 1
## INS-IGF2 0 0 0 0 0 1
## IGF2-AS 0 0 0 0 0 0
## INS 0 0 0 0 0 0
## STIM1 1517 928 1181 1128 1152 1430
## TRIM22 5743 3605 2341 1179 3010 1400
## PTH 0 0 0 0 0 0
## SAA1 0 0 1 0 0 1
## SLC1A2 0 6 2 4 4 0
## FOSL1 130 283 87 172 79 55
## CCND1 7 6 9 4 4 4
## JRKL 99 32 73 30 83 51
## MMP7 0 0 0 0 0 1
## MMP1 2 0 1 18 11 0
## MMP3 0 0 0 0 0 0
## CASP1 3183 1993 2290 1729 3063 1594
## DLAT 234 68 85 82 130 171
## IL18 100 27 130 145 117 71
## CD3E 4042 1826 1726 2962 2144 4109
## MCAM 204 185 324 253 274 202
## WNK1 4306 3218 4345 3255 3037 3146
## TNFRSF1A 3130 2332 2704 1775 2713 1437
## GAPDH 19212 15522 15500 30598 19052 20914
## CD4 3908 1641 2252 1936 3672 3401
## SLC2A3 8458 19415 7925 14584 11219 8951
## CLEC4D 394 390 871 259 496 223
## KLRB1 878 583 736 306 723 1363
## CD69 3161 6225 7577 5674 3819 3330
## CLEC2B 2013 1877 1361 2147 1642 957
## OLR1 11 23 16 207 5 5
## ABCD2 239 121 144 142 171 122
## LRRK2 5556 8094 9950 6048 7660 2936
## VDR 333 429 449 429 225 270
## TMBIM6 13663 9729 11960 10223 12505 9383
## PFDN5 3613 1823 2433 4439 3606 3737
## SP7 0 0 0 0 0 0
## MUCL1 0 0 2 0 0 0
## CD63 2978 3243 3840 5039 3207 2256
## SUOX 966 531 905 735 775 644
## RPS26 831 2348 2763 8188 3166 4172
## RPL41 8860 4656 5425 10038 7228 9371
## IL23A 35 21 19 23 25 33
## DDIT3 350 970 831 801 479 322
## IFNG 80 96 161 42 53 76
## IL22 2 3 2 6 0 0
## LYZ 81699 23110 57089 131163 139099 28887
## CAPS2 4 0 7 3 9 2
## SYT1 5 0 11 2 1 0
## BTG1 8218 12034 17778 11739 11676 17118
## HCAR3 2591 6388 6922 3580 5229 1757
## GJB2 1 6 2 0 4 11
## GJB6 15 91 25 29 16 62
## TNFSF11 4 0 6 5 5 3
## TPT1 61663 34093 39686 77239 53955 57853
## LMO7 59 39 44 53 57 39
## TNFSF13B 4056 3012 1388 1130 2030 1500
## LAMP1 2746 2396 2554 2706 2827 2452
## PSME2 1649 979 1038 906 1751 1293
## GZMB 1732 638 1528 299 1060 2880
## RPL36AL 2829 1867 1895 3269 2263 2170
## PYGL 3331 5143 3809 5737 4603 1941
## HIF1A 2071 4514 4666 4197 3335 2362
## FOS 38016 129899 180469 60580 110134 72375
## JDP2 570 936 1794 954 569 858
## NOXRED1 13 13 25 6 4 8
## SERPINA1 22907 22277 22443 23936 25192 13797
## CDC42BPB 221 135 185 218 244 248
## PLA2G4D 0 0 0 0 0 0
## TRIM69 24 14 13 22 14 4
## SLC51B 0 0 0 0 0 0
## SMAD3 673 402 451 445 587 789
## CYP1A1 0 0 0 1 1 1
## AKAP13 4076 4765 5992 4443 4738 4441
## MEFV 2115 1585 1828 1802 1757 1038
## SOCS1 166 112 213 249 149 229
## ATXN2L 1737 1153 1457 1604 1411 1776
## CD19 97 98 27 30 156 104
## ITGAL 6973 4475 4477 4143 5355 6175
## ITGAM 5037 5736 5165 6317 5400 3696
## ITGAX 3396 6288 8472 4825 6153 2866
## DNAJA2 643 503 694 643 515 553
## SIAH1 105 105 168 102 100 95
## ADCY7 2780 1858 2334 1572 2513 2345
## NOD2 847 509 1068 456 1169 373
## CMTM2 1490 2863 2492 2324 2090 1312
## SF3B3 1099 497 680 498 805 771
## PSMD7 724 522 571 891 652 675
## WWOX 46 32 34 35 33 43
## MAF 781 338 445 280 471 936
## SLC7A5 489 569 465 795 290 1012
## CXCL16 1339 2552 3025 2625 2604 2982
## XAF1 2978 1690 703 208 1163 534
## CD68 3757 2023 2243 3111 4470 3535
## PER1 405 1260 6195 3279 1324 2932
## NOS2 1 3 3 1 4 0
## TRAF4 76 93 104 77 99 174
## CCL2 143 15 2 2 32 0
## CCL5 8175 3240 3236 3370 3606 9635
## CCL3 550 505 811 743 623 249
## CCR7 484 422 497 596 554 296
## STAT3 3934 3591 3855 3616 3147 2205
## SOST 0 0 0 0 0 0
## ITGA2B 816 557 155 2363 412 307
## EFCAB13 15 22 24 13 21 23
## NPEPPS 682 652 985 646 742 454
## TBX21 588 219 428 134 321 698
## COL1A1 0 4 3 1 1 1
## MRPS23 180 56 57 108 98 132
## MIR21 5 3 8 3 1 2
## RPS6KB1 407 251 311 248 356 330
## ACE 93 26 66 102 50 75
## ERN1 1138 887 2284 1277 1139 1547
## PRTN3 6 39 120 658 2 3
## PLIN5 53 99 174 102 85 57
## RETN 55 99 108 685 26 78
## CCL25 3 0 0 0 2 0
## ICAM1 1783 4956 3556 7201 2948 1358
## TYK2 1461 1419 1779 1243 1344 1029
## SMARCA4 697 426 468 578 489 729
## ACP5 435 98 117 310 218 352
## JUNB 25660 40126 46069 55661 25190 43285
## CYP4F22 58 9 40 8 174 64
## JAK3 1740 2383 2689 2121 1657 975
## JUND 7252 19504 24436 15588 12742 17190
## CEBPA 634 461 480 809 912 483
## CEBPG 303 151 217 234 228 255
## ACP7 0 0 3 0 1 1
## ZFP36 23714 61947 75564 68643 30266 24067
## TGFB1 5145 4460 3736 6595 3596 5147
## RPS19 11647 5935 7458 15408 9277 13824
## PSG2 0 0 0 0 0 0
## FUT2 2 3 3 2 1 2
## NKG7 9727 3503 4595 3300 3719 9679
## ZNF415 6 2 14 0 9 3
## LILRB2 4166 4704 5567 4144 4741 4459
## LILRA5 2870 3464 1448 2750 2519 2776
## KIR3DL1 112 15 101 23 39 225
## KIR3DL2 39 16 53 14 20 137
## SMOX 103 81 94 169 60 93
## BMP2 5 20 10 20 4 1
## GINS1 14 4 4 10 8 10
## PLCG1 810 442 609 559 510 589
## YWHAB 6006 4317 3943 4992 5708 5028
## PI3 856 916 3227 1245 1059 614
## MMP9 2589 3614 3374 4861 2265 1404
## CD40 249 56 46 82 190 165
## PFDN4 48 35 41 63 42 58
## BMP7 0 0 0 0 0 0
## RPS21 5230 1642 3303 6620 4138 6035
## MX1 7605 2209 965 209 1687 508
## PFKL 1365 561 760 760 1053 1232
## IL17RA 4467 5129 5735 5994 4658 2581
## UBE2L3 1189 566 612 914 769 840
## TPST2 1776 1087 1435 1576 1005 1748
## XBP1 1669 610 956 1353 756 998
## UQCR10 684 350 388 542 477 492
## SEC14L2 29 26 24 52 24 38
## APOL6 2547 2205 1468 669 1883 1048
## APOL1 913 681 643 281 858 462
## TYMP 4398 3091 2874 2645 4900 3120
## BEND2 40 48 47 50 43 46
## PHEX 10 8 3 3 7 6
## TIMP1 1692 1083 1896 2057 1262 2038
## FOXP3 177 36 53 36 49 113
## MSN 23061 19501 21320 22699 21471 19838
## PGK1 7355 7067 7108 8866 8917 7076
## LAMP2 5972 5917 7682 5933 5607 3225
## CD40LG 137 38 92 48 83 88
## IRAK1 1374 1129 1483 1690 1440 1550
## COX2 57762 34006 35662 68548 46658 71560
## GSM3308473 GSM3308474 GSM3308475 GSM3308476 GSM3308477 GSM3308478
## TNFRSF9 49 68 69 107 111 68
## ENO1 7354 3626 6669 5434 6071 6647
## PIK3CD 6613 6162 5760 5003 7728 6213
## PGD 7186 8038 3806 4271 5972 5718
## MTHFR 365 157 520 414 487 336
## TNFRSF1B 16274 12808 14304 9864 15244 14301
## PINK1 1047 978 601 642 838 947
## IFNLR1 60 13 48 51 40 48
## RUNX3 4051 968 2757 2250 2656 4036
## SH3BGRL3 13114 8673 8598 6741 10969 10870
## CD52 3728 1391 4954 2744 3523 3789
## IFI6 1756 1910 5111 1439 910 5129
## ZC3H12A 324 493 483 630 648 530
## UTP11 123 54 86 56 61 85
## JUN 333 2622 3712 8215 15481 8201
## KANK4 0 0 0 1 0 0
## EFCAB7 22 13 25 31 18 22
## IL23R 1 0 3 0 8 0
## ADGRL2 0 0 0 0 0 0
## GBP3 200 45 276 217 64 203
## GBP1 1798 1691 2341 658 529 1583
## GBP5 3845 4726 6616 2281 1427 3839
## TGFBR3 965 184 439 342 444 748
## VCAM1 1 2 0 2 0 2
## PTPN22 475 207 256 242 246 333
## CD160 225 23 114 83 114 126
## FCGR1A 718 1947 2805 539 654 889
## MCL1 17357 34811 20459 21450 28531 26941
## CTSK 29 18 66 45 44 65
## RORC 42 2 57 23 45 30
## S100A9 112504 243670 117314 95407 140171 102096
## S100A12 3336 9862 2895 3653 3469 3632
## S100A8 38854 99115 41982 38585 50907 33455
## IL6R 5694 4394 3796 3596 5035 3901
## RIT1 1253 2053 1217 1178 1667 1430
## BGLAP 8 4 8 5 3 5
## IFI16 3532 4139 5206 1478 2078 3922
## AIM2 147 437 363 64 96 235
## CRP 0 0 0 0 0 0
## FCGR2A 13784 18369 16411 8214 16892 11982
## HSPA6 5145 2076 2632 1201 2237 2446
## FCGR3A 27644 19946 23202 7325 17207 23682
## SELL 41107 69050 35846 29377 37359 53257
## GLUL 12178 26637 12482 12174 16274 13963
## PTGS2 3225 8573 2584 19954 14919 9108
## CRB1 0 0 2 0 0 0
## KDM5B 416 438 404 457 495 452
## IL10 1 9 11 4 0 6
## YOD1 191 297 325 237 186 295
## HHAT 36 12 51 32 27 27
## TRAF5 251 94 333 328 291 285
## NLRP3 811 425 808 897 1188 709
## LINC01250 0 0 0 0 0 0
## RPS7 8152 3299 10294 6429 6784 7915
## RSAD2 912 1671 6570 1100 261 4803
## FOSL2 2946 5654 2801 3750 4697 3156
## REL 945 796 1204 1198 1060 1096
## TGFA 523 1376 441 370 540 493
## DYSF 4759 9430 4772 4078 5135 5125
## HK2 1069 1066 737 822 861 841
## CD8A 1895 347 1200 553 644 2344
## CD8B 613 131 927 504 303 944
## EIF5B 512 151 468 330 331 470
## IL1R1 166 637 136 279 285 304
## RGPD6 68 34 77 64 49 70
## IL1A 0 0 0 2 1 0
## IL1B 431 288 680 1379 1425 597
## IL37 0 0 0 0 0 0
## IL36RN 0 0 0 0 0 0
## IL1F10 0 0 0 0 0 0
## IL1RN 3236 3287 3733 3393 3739 3984
## NMI 1903 2868 2132 869 1300 2199
## TNFAIP6 650 1044 820 576 266 435
## IFIH1 522 394 1025 377 305 734
## SCN1A 0 0 0 0 0 0
## ABCB11 0 0 0 1 1 2
## RBM45 68 24 63 44 61 54
## FRZB 0 0 0 0 0 0
## TFPI 20 9 5 3 3 6
## STAT1 5697 5164 6476 2717 2894 5931
## NABP1 437 911 563 862 721 503
## SF3B1 3923 3565 3741 3326 3721 3993
## CASP10 340 208 381 354 330 411
## CD28 498 99 846 484 489 561
## CTLA4 34 24 93 47 58 48
## ICOS 143 48 240 102 122 110
## NDUFS1 556 299 539 363 420 553
## CXCR2 27876 25659 17658 9896 22239 14826
## IRS1 44 41 92 96 72 85
## CCL20 1 2 2 3 2 3
## ATG16L1 212 102 277 253 257 293
## GPR35 91 42 112 88 110 134
## PDCD1 41 13 31 27 19 33
## PPARG 6 5 6 0 1 2
## RPL15 14669 4770 16737 10675 11342 12893
## EOMES 263 20 50 85 78 143
## CX3CR1 2630 164 1321 747 847 1664
## ACKR2 2 0 0 1 0 0
## CCR2 1182 234 763 432 592 756
## CCRL2 35 25 71 34 42 23
## TLR9 94 70 62 69 56 40
## ARHGEF3 1043 362 1362 949 1027 1369
## ADAMTS9 0 0 0 0 1 0
## TMEM45A 3 2 2 1 3 1
## CD80 2 2 5 16 4 5
## CD86 1111 330 973 526 898 796
## MIX23 31 9 38 7 23 20
## PLS1 26 4 15 12 7 21
## PTX3 39 54 81 96 69 55
## GOLIM4 96 36 78 68 75 95
## MYNN 277 331 311 308 372 318
## TNFSF10 4272 3482 5128 1862 2336 4621
## ADIPOQ 0 0 0 0 0 0
## SPON2 890 165 426 152 505 904
## S100P 3650 4493 1238 1436 4145 3473
## WDR1 8241 5378 4763 3604 5561 6750
## CD38 403 256 293 197 176 283
## PPARGC1A 2 3 0 3 6 0
## TMPRSS11B 0 0 0 0 0 0
## CSN3 0 0 0 0 0 0
## ALB 0 0 0 0 0 0
## CXCL8 13960 34386 13415 83592 95007 35672
## CXCL2 0 4 6 43 42 33
## AREG 3 141 21 44 20 61
## CXCL10 44 7 65 13 20 34
## CXCL13 1 3 1 0 0 0
## SPP1 21 189 19 49 157 5
## HERC6 199 110 322 160 156 341
## NFKB1 942 573 890 642 698 783
## SEC24B 535 410 390 355 398 483
## EGF 91 35 47 7 22 87
## IL2 0 0 0 0 0 0
## IL21 1 1 0 0 0 1
## IL21-AS1 2 1 1 0 2 2
## SLC7A11 25 15 11 9 19 6
## IL15 88 42 69 58 42 85
## EDNRA 0 0 0 0 0 0
## TLR2 3642 9907 4376 3165 3471 4930
## FGB 0 0 0 0 0 0
## DDX60 499 516 1437 499 260 1100
## SPCS3 2393 1758 1984 1454 1682 1945
## TLR3 22 0 7 5 5 13
## OSMR 25 39 31 30 23 38
## GZMK 605 199 407 351 337 487
## GZMA 1582 306 679 510 804 1208
## ANKRD55 84 53 86 56 47 85
## CENPK 104 30 91 48 50 73
## CAST 3233 1265 2581 2389 2428 2483
## ERAP1 1740 658 1442 1134 1128 1435
## ERAP2 125 1607 3433 1132 1098 1892
## TNFAIP8 1579 697 1348 986 1096 1382
## CSF2 1 0 0 0 0 0
## IL5 0 0 0 0 0 3
## IL13 0 1 0 0 0 1
## IL4 4 1 2 2 3 1
## CD14 7491 6696 8639 6183 12078 8719
## CSNK1A1 2047 1337 1737 1063 1506 1575
## PPARGC1B 100 47 226 150 132 202
## TNIP1 4920 5616 5068 3665 4911 4563
## ATOX1 232 141 152 147 157 211
## FAXDC2 372 110 246 105 137 324
## IL12B 1 1 3 2 2 1
## MIR146A 0 0 0 0 0 0
## PDLIM7 1747 2073 1393 1261 2123 1740
## SERPINB1 4269 7121 5405 3405 5450 4206
## SSR1 2717 1931 2489 1417 1858 2285
## CD83 304 111 626 846 851 336
## SOX4 117 106 172 130 127 239
## CMAHP 79 35 93 106 61 81
## HLA-A 55916 46739 49914 30731 39581 44376
## HLA-C 82558 110779 79036 77176 88307 110753
## HLA-B 109125 125402 129118 79308 91627 107900
## MICA 128 37 168 122 138 131
## LTA 59 5 79 42 57 52
## TNF 139 59 193 68 156 287
## HLA-DRB1 2900 1541 3385 4618 3236 3490
## HLA-DQB1 388 157 479 883 3618 2465
## PPARD 217 115 340 242 260 263
## CCND3 4899 5716 3860 3033 3176 6251
## VEGFA 110 92 165 96 143 98
## RUNX2 399 551 456 394 433 538
## IL17A 0 0 0 0 0 0
## IL17F 0 0 0 0 0 0
## PRDM1 699 694 630 333 390 778
## ATG5 462 258 357 294 329 464
## TRAF3IP2 185 89 232 153 144 188
## NCOA7 388 237 464 272 221 303
## SGK1 3520 1156 2349 1870 3172 3004
## IFNGR1 4078 4628 2724 1444 2837 2776
## TNFAIP3 1537 9256 4021 6176 5102 4740
## SOD2 41661 68419 43488 31642 47692 32125
## LPAL2 7 3 9 16 14 17
## PLG 0 0 0 1 0 0
## CCR6 75 23 92 79 72 41
## RAC1 3471 2140 2375 1647 3438 2832
## ZNF316 694 511 728 543 849 788
## AHR 467 504 1338 1239 992 871
## IL6 0 0 5 6 2 7
## TOMM7 1878 777 2693 1727 1499 2171
## CYCS 577 268 644 480 687 684
## AQP1 0 2 5 6 4 6
## NT5C3A 1131 1031 1137 620 555 1183
## EGFR 0 0 0 0 0 0
## CD36 2287 809 3475 1795 2481 2394
## SAMD9 1855 2050 2969 1773 1370 2923
## SERPINE1 13 3 12 6 11 19
## CUX1 1537 1619 1542 1246 1834 2009
## PSMC2 446 161 313 222 286 372
## NAMPT 43789 104711 56383 30419 57487 47580
## HYAL4 0 1 0 0 0 0
## LEP 15 0 5 0 3 3
## CALD1 40 11 11 2 21 41
## BRAF 543 566 645 629 649 723
## EZH2 55 34 53 67 57 47
## DNAJB6 1768 1682 1139 740 1421 1472
## CSMD1 0 1 6 1 2 2
## CTSB 6130 4086 7994 4045 4494 5136
## EGR3 227 455 330 498 941 497
## TNFRSF10A 99 41 227 143 118 161
## BNIP3L 2560 2407 2108 1623 2570 2152
## DUSP4 28 33 39 38 49 14
## NRG1 140 89 95 142 113 55
## RPL7 9400 3228 12142 7281 7598 9173
## IL7 11 8 13 9 11 8
## GEM 0 1 0 2 2 0
## MYC 608 195 1106 282 329 1146
## GPT 2 0 3 0 1 0
## JAK2 1127 1188 1171 904 1027 1193
## CD274 164 379 723 72 133 182
## IL33 0 0 0 0 0 0
## LURAP1L-AS1 0 0 0 0 0 0
## LURAP1L 8 0 1 0 1 3
## TTC39B 109 48 212 171 110 169
## IFNA1 0 0 0 0 0 0
## TEK 13 20 26 4 8 16
## TRBV20OR9-2 0 0 0 0 0 0
## TOMM5 237 86 237 138 178 196
## ANXA1 4753 5041 5306 5802 6248 6309
## ERP44 1389 1400 1399 1046 1236 1412
## ZNF483 17 3 38 34 27 31
## TNFSF15 7 5 6 16 8 1
## TLR4 7552 12677 6100 4645 8786 6073
## PTGS1 1913 517 778 404 690 1613
## HSPA5 4742 4746 4237 6889 5164 5133
## FNBP1 4355 2739 3372 2249 2890 3672
## CARD9 193 71 164 99 165 174
## TRAF2 134 44 116 84 106 118
## CLIC3 264 32 62 76 147 149
## IL2RA 96 28 144 65 91 106
## GATA3 309 62 301 219 304 229
## VIM 15799 13074 16462 13965 19218 19685
## CREM 172 206 174 129 139 152
## DKK1 0 0 0 0 0 0
## MBL2 0 0 0 0 0 0
## SAR1A 928 695 664 650 666 830
## PRF1 3881 632 1288 1079 1683 3332
## ZMIZ1 1884 1570 2251 1683 2431 2650
## IFIT3 5933 7585 20598 4748 2786 19276
## TALDO1 12172 12953 7335 6079 10157 8385
## IGF2 1 0 0 0 1 0
## INS-IGF2 1 0 0 0 1 0
## IGF2-AS 0 0 0 0 0 0
## INS 0 0 0 0 0 0
## STIM1 1617 824 1177 894 1230 1581
## TRIM22 2998 6824 5813 2252 1820 6133
## PTH 0 0 0 0 0 0
## SAA1 0 0 1 0 0 0
## SLC1A2 0 4 2 1 0 2
## FOSL1 5 34 35 64 73 34
## CCND1 3 3 4 4 7 6
## JRKL 90 28 91 75 61 54
## MMP7 0 0 0 1 0 0
## MMP1 1 2 7 0 2 4
## MMP3 0 0 0 0 0 0
## CASP1 3243 4032 3990 2037 2557 3274
## DLAT 197 63 215 114 149 179
## IL18 121 76 113 79 108 74
## CD3E 3016 601 3892 1881 2151 3085
## MCAM 220 190 244 256 245 255
## WNK1 4294 2403 3718 2698 3500 4103
## TNFRSF1A 4509 4112 4116 2039 4483 3486
## GAPDH 16554 16366 18568 15341 18327 17603
## CD4 3642 1356 5188 2149 3466 3175
## SLC2A3 6167 16274 8675 6853 10485 9781
## CLEC4D 288 1209 256 467 478 605
## KLRB1 1258 409 950 499 605 779
## CD69 385 602 1805 2184 2182 2411
## CLEC2B 1828 1943 2530 1433 1674 1646
## OLR1 21 8 23 59 15 7
## ABCD2 128 34 212 152 120 188
## LRRK2 10297 11579 6698 7091 7937 9576
## VDR 753 389 446 404 373 365
## TMBIM6 15902 13164 11897 8424 13691 13502
## PFDN5 3326 1661 3804 2491 2955 3272
## SP7 0 1 0 0 0 0
## MUCL1 0 0 0 0 0 0
## CD63 3172 3431 2679 1932 2767 2801
## SUOX 1296 954 872 779 1059 1016
## RPS26 3423 454 7623 2566 2765 3501
## RPL41 7238 3207 8737 5747 6196 7133
## IL23A 17 11 38 26 33 43
## DDIT3 350 639 537 607 713 614
## IFNG 8 11 13 28 79 64
## IL22 0 0 0 1 0 1
## LYZ 45380 49267 41434 29234 35023 100686
## CAPS2 1 1 5 6 2 3
## SYT1 6 2 1 11 5 4
## BTG1 7750 11142 8477 7188 8179 10824
## HCAR3 3500 3052 3959 1730 4007 2206
## GJB2 0 2 0 1 1 3
## GJB6 5 62 17 40 15 15
## TNFSF11 0 0 3 2 5 0
## TPT1 55889 26642 62528 37984 48186 53195
## LMO7 55 11 93 58 39 63
## TNFSF13B 2067 3783 4179 2551 2456 2869
## LAMP1 3121 2490 2475 2148 2935 2845
## PSME2 1589 1192 1829 890 932 1806
## GZMB 1852 267 487 608 640 1075
## RPL36AL 2254 1594 1944 1689 1773 1909
## PYGL 5457 11141 3328 2985 5063 4885
## HIF1A 1670 3970 2255 2347 2253 2513
## FOS 3307 98136 19325 35592 65737 44138
## JDP2 730 1436 485 607 674 918
## NOXRED1 3 10 7 2 10 9
## SERPINA1 19419 35587 30512 16440 22309 23571
## CDC42BPB 184 59 288 146 283 218
## PLA2G4D 0 0 0 0 0 0
## TRIM69 18 13 26 18 11 21
## SLC51B 0 0 0 0 0 0
## SMAD3 571 178 662 443 491 503
## CYP1A1 0 0 1 0 2 1
## AKAP13 4337 5695 4727 3180 3949 5232
## MEFV 3887 3105 3142 1558 2631 3432
## SOCS1 33 93 94 42 128 126
## ATXN2L 1563 633 2027 1419 1503 1696
## CD19 93 61 110 127 92 56
## ITGAL 5975 2897 5282 3875 4614 6289
## ITGAM 5067 7574 3924 4606 5349 5309
## ITGAX 3706 5996 3321 4446 4165 4809
## DNAJA2 791 583 577 420 555 622
## SIAH1 112 87 103 105 84 121
## ADCY7 2881 1376 2820 2176 2351 2859
## NOD2 409 1171 1197 429 433 917
## CMTM2 2326 4413 1526 2055 2831 2325
## SF3B3 911 208 1011 798 701 861
## PSMD7 764 479 613 508 621 645
## WWOX 37 19 42 31 43 54
## MAF 597 192 580 303 406 423
## SLC7A5 206 267 320 153 171 233
## CXCL16 1551 4347 1436 2073 2096 1918
## XAF1 831 1396 3164 908 543 2532
## CD68 4813 2153 4731 1822 3772 4023
## PER1 177 2306 577 608 598 787
## NOS2 0 0 3 0 2 0
## TRAF4 84 28 90 85 63 71
## CCL2 20 1 6 7 22 16
## CCL5 6484 1252 2471 1752 2309 4821
## CCL3 81 76 190 296 469 278
## CCR7 678 79 1108 560 426 906
## STAT3 6208 6090 5113 2825 4609 5020
## SOST 0 0 0 0 0 0
## ITGA2B 2146 275 543 127 452 1627
## EFCAB13 10 6 22 18 14 12
## NPEPPS 1038 717 725 675 861 832
## TBX21 570 64 171 189 319 429
## COL1A1 0 0 0 1 0 0
## MRPS23 238 59 163 87 114 174
## MIR21 7 9 1 5 7 6
## RPS6KB1 348 230 372 245 306 371
## ACE 14 7 81 26 48 29
## ERN1 839 978 749 1325 1042 1253
## PRTN3 21 9 14 223 66 11
## PLIN5 87 151 96 102 112 114
## RETN 88 56 57 238 70 42
## CCL25 0 0 0 0 1 0
## ICAM1 1146 2420 1936 1529 1694 1207
## TYK2 1966 1190 1365 1336 1575 1481
## SMARCA4 694 243 728 422 624 669
## ACP5 318 234 329 220 173 192
## JUNB 10319 43313 24353 16441 36807 34451
## CYP4F22 68 6 60 4 27 38
## JAK3 1164 1838 1974 2010 1487 1331
## JUND 3150 5046 5770 7879 12970 8906
## CEBPA 970 656 703 460 849 971
## CEBPG 298 132 304 237 249 281
## ACP7 1 0 0 0 0 4
## ZFP36 6117 28576 17879 18584 33540 28502
## TGFB1 6631 4314 5003 2492 4538 5895
## RPS19 10293 3160 12141 7383 8492 9782
## PSG2 0 0 0 0 0 0
## FUT2 3 1 1 3 1 2
## NKG7 7340 1129 1963 2506 2738 6180
## ZNF415 11 7 3 16 5 3
## LILRB2 3522 3487 3603 2778 5565 4420
## LILRA5 3194 3124 1519 2331 4482 2319
## KIR3DL1 252 22 16 56 161 29
## KIR3DL2 149 41 73 7 53 78
## SMOX 302 92 127 45 79 200
## BMP2 6 5 1 8 20 5
## GINS1 23 6 13 3 4 8
## PLCG1 588 140 976 598 465 735
## YWHAB 6734 6084 5066 3600 5301 5675
## PI3 395 1066 653 876 1673 644
## MMP9 1483 10778 866 1796 2012 2598
## CD40 141 38 275 129 105 105
## PFDN4 62 19 43 44 45 34
## BMP7 0 0 0 0 0 0
## RPS21 4532 1572 5290 3422 3599 3867
## MX1 2114 1698 6528 2114 987 4989
## PFKL 1299 518 1264 682 987 1181
## IL17RA 6816 7696 4726 4385 5704 5912
## UBE2L3 1415 790 970 628 913 1030
## TPST2 1523 561 1130 795 1280 1619
## XBP1 1691 675 977 720 750 1009
## UQCR10 757 343 555 375 519 542
## SEC14L2 19 6 62 27 16 50
## APOL6 2253 2366 3709 1207 1016 2812
## APOL1 856 904 1235 395 532 807
## TYMP 4615 4130 5303 2166 3580 5974
## BEND2 73 52 51 15 51 124
## PHEX 15 6 21 6 11 8
## TIMP1 1790 1028 1239 1716 1965 1530
## FOXP3 59 10 90 59 67 45
## MSN 29272 23663 20212 17746 24291 27058
## PGK1 6556 9018 7202 6292 8259 8013
## LAMP2 7968 10084 6093 5033 7004 6600
## CD40LG 144 22 164 86 121 118
## IRAK1 1466 929 1487 1121 1451 1768
## COX2 42577 30923 51614 38148 39017 53421
## GSM3308479 GSM3308480 GSM3308481 GSM3308482 GSM3308483 GSM3308484
## TNFRSF9 76 141 96 67 54 165
## ENO1 4239 5417 7166 7280 6460 7493
## PIK3CD 7748 6449 6347 4935 4400 7453
## PGD 6270 7853 6213 5045 3256 7933
## MTHFR 310 329 490 412 429 251
## TNFRSF1B 13659 15086 14604 17217 10640 15233
## PINK1 1000 1102 805 646 593 1175
## IFNLR1 7 23 60 73 63 51
## RUNX3 1578 2660 2063 7677 7023 2202
## SH3BGRL3 10057 10035 10234 13008 10675 11299
## CD52 1524 870 4024 4607 5817 4205
## IFI6 528 13513 1025 3411 1800 644
## ZC3H12A 602 394 189 536 310 440
## UTP11 73 54 128 90 119 93
## JUN 8098 5534 839 5141 1617 434
## KANK4 0 0 0 0 0 0
## EFCAB7 17 18 39 18 39 23
## IL23R 1 0 3 1 4 6
## ADGRL2 1 0 0 0 0 0
## GBP3 87 167 625 200 276 188
## GBP1 515 1878 3435 1331 887 602
## GBP5 1317 2840 7826 3589 2108 1433
## TGFBR3 351 295 355 1702 2164 342
## VCAM1 1 0 2 8 1 1
## PTPN22 211 236 529 387 571 349
## CD160 143 92 29 253 252 58
## FCGR1A 449 677 1782 1165 482 1393
## MCL1 44213 37895 20011 17398 16557 17498
## CTSK 23 54 36 43 45 25
## RORC 16 2 102 65 76 72
## S100A9 180814 195635 119661 93553 61372 219679
## S100A12 4730 7305 5628 2351 1527 8556
## S100A8 66810 83323 46202 34890 22805 86146
## IL6R 5092 4826 6486 4136 3175 6409
## RIT1 2212 1270 1211 1109 949 1660
## BGLAP 6 3 4 6 9 7
## IFI16 3679 5162 4415 3045 2750 4275
## AIM2 204 279 391 143 89 259
## CRP 0 0 0 0 0 0
## FCGR2A 15552 11228 11047 11536 5991 17880
## HSPA6 2287 1797 1660 1499 1025 1930
## FCGR3A 23106 22896 19352 20338 14284 17463
## SELL 59941 68748 52779 33463 28916 47567
## GLUL 22047 14484 9643 12521 8588 15721
## PTGS2 16894 11861 10153 2379 1204 3358
## CRB1 1 1 2 2 1 1
## KDM5B 667 540 385 352 326 426
## IL10 7 8 1 5 4 0
## YOD1 445 269 164 242 223 194
## HHAT 9 22 29 45 46 37
## TRAF5 94 102 241 251 491 266
## NLRP3 746 847 898 911 644 531
## LINC01250 0 0 0 0 0 1
## RPS7 4187 3787 8325 7762 13122 9828
## RSAD2 155 9417 535 1548 838 135
## FOSL2 4378 3834 2720 4308 3685 3549
## REL 874 730 1043 1229 1059 905
## TGFA 844 493 456 329 296 632
## DYSF 8075 9367 6383 4066 2406 8761
## HK2 1486 2235 1822 831 647 1362
## CD8A 429 409 1314 4023 1900 1263
## CD8B 113 109 592 1248 874 1088
## EIF5B 204 177 699 450 770 516
## IL1R1 713 416 160 187 119 239
## RGPD6 41 31 90 56 98 71
## IL1A 3 0 0 0 0 0
## IL1B 1915 183 506 360 181 548
## IL37 0 0 0 1 0 0
## IL36RN 0 0 0 0 0 0
## IL1F10 0 0 0 0 0 0
## IL1RN 3478 3802 1863 2581 1359 3253
## NMI 2040 1859 1796 1359 1349 1880
## TNFAIP6 1240 797 245 388 169 440
## IFIH1 226 1107 509 487 378 292
## SCN1A 0 0 0 0 0 0
## ABCB11 1 1 0 1 0 0
## RBM45 22 23 75 44 78 44
## FRZB 0 0 0 0 0 1
## TFPI 4 1 2 3 3 6
## STAT1 3908 6206 9625 5055 3852 3163
## NABP1 1112 744 543 374 265 497
## SF3B1 3995 3245 3872 3964 4719 4282
## CASP10 283 433 432 369 387 275
## CD28 126 73 730 525 824 512
## CTLA4 24 27 32 96 105 72
## ICOS 28 19 207 164 327 166
## NDUFS1 425 407 656 554 632 539
## CXCR2 27230 15511 15104 14900 8604 22579
## IRS1 24 28 88 52 96 81
## CCL20 45 0 0 1 0 0
## ATG16L1 221 186 285 302 402 239
## GPR35 48 109 87 147 139 118
## PDCD1 10 25 36 58 59 27
## PPARG 11 5 3 9 3 2
## RPL15 6303 5848 14793 14626 20996 15657
## EOMES 57 85 104 241 257 66
## CX3CR1 704 900 2352 2069 1357 963
## ACKR2 0 1 1 3 2 0
## CCR2 484 628 2437 868 443 950
## CCRL2 27 29 46 44 38 24
## TLR9 62 65 63 54 44 81
## ARHGEF3 588 848 1151 1340 1628 742
## ADAMTS9 0 0 0 0 0 0
## TMEM45A 21 4 4 4 3 8
## CD80 0 2 6 6 7 1
## CD86 439 720 1691 1143 833 674
## MIX23 14 5 42 19 36 21
## PLS1 6 4 24 24 30 15
## PTX3 88 57 47 52 48 48
## GOLIM4 57 49 158 102 83 78
## MYNN 322 207 315 330 355 328
## TNFSF10 3391 5631 5436 2439 1843 3556
## ADIPOQ 0 0 0 0 0 0
## SPON2 740 1659 102 1494 1534 135
## S100P 9018 3021 1779 1726 2327 2615
## WDR1 6544 6278 6424 6337 5518 6097
## CD38 131 262 258 375 346 271
## PPARGC1A 2 0 20 0 6 9
## TMPRSS11B 0 0 0 0 0 0
## CSN3 0 0 0 0 0 0
## ALB 0 0 0 0 0 0
## CXCL8 141249 17292 11250 15401 4842 11886
## CXCL2 77 8 7 2 1 2
## AREG 328 386 2 97 79 1
## CXCL10 14 29 51 28 27 16
## CXCL13 0 0 1 1 1 0
## SPP1 194 30 77 26 79 50
## HERC6 90 688 194 257 335 162
## NFKB1 598 560 1314 802 924 1228
## SEC24B 495 343 485 407 450 371
## EGF 43 22 23 21 21 26
## IL2 1 1 1 0 0 0
## IL21 0 1 3 0 0 2
## IL21-AS1 0 1 3 0 0 5
## SLC7A11 42 4 20 17 3 31
## IL15 55 84 190 95 90 64
## EDNRA 0 0 0 0 0 0
## TLR2 15386 7839 3409 3548 2081 4873
## FGB 0 0 0 0 0 0
## DDX60 195 1884 582 667 557 243
## SPCS3 1761 925 2532 1817 2475 2196
## TLR3 2 1 29 11 25 5
## OSMR 32 22 28 36 23 21
## GZMK 120 125 641 968 1272 659
## GZMA 580 630 756 2091 2481 653
## ANKRD55 73 77 74 53 136 74
## CENPK 22 6 112 42 131 99
## CAST 1827 2001 3885 3621 3899 3138
## ERAP1 741 832 2004 1386 1753 1729
## ERAP2 1633 153 185 3760 2214 1287
## TNFAIP8 888 548 1716 1266 1977 1475
## CSF2 0 0 0 0 0 0
## IL5 0 0 1 0 1 0
## IL13 0 0 0 1 0 0
## IL4 1 2 2 1 2 3
## CD14 3421 5263 7872 8986 6119 10663
## CSNK1A1 1505 1336 2168 1435 1641 1680
## PPARGC1B 110 213 132 108 118 85
## TNIP1 4975 4751 4151 4353 3389 6493
## ATOX1 156 202 209 185 183 170
## FAXDC2 101 115 188 124 156 161
## IL12B 4 2 0 1 1 1
## MIR146A 0 0 0 0 0 0
## PDLIM7 2588 2279 1172 1414 804 1710
## SERPINB1 5683 6053 3991 4603 3466 6193
## SSR1 1786 1313 3144 2395 2713 2580
## CD83 240 248 347 556 683 281
## SOX4 140 225 160 112 90 118
## CMAHP 34 40 56 62 122 59
## HLA-A 46475 50566 45181 46462 36938 41412
## HLA-C 99687 114247 62213 109946 63631 62308
## HLA-B 121993 135042 107404 103946 93755 72727
## MICA 76 95 228 92 128 113
## LTA 25 15 82 45 77 70
## TNF 187 64 237 326 117 235
## HLA-DRB1 2806 3641 5789 5492 3592 1616
## HLA-DQB1 1724 797 614 2708 395 199
## PPARD 170 134 322 383 372 296
## CCND3 10333 9775 3672 4897 5660 4008
## VEGFA 168 175 155 223 73 113
## RUNX2 567 338 343 333 572 375
## IL17A 0 0 0 0 0 0
## IL17F 0 0 0 0 0 0
## PRDM1 1024 619 618 891 1029 312
## ATG5 304 236 482 377 532 359
## TRAF3IP2 91 156 166 157 268 207
## NCOA7 246 283 604 434 611 358
## SGK1 1842 1280 3520 2466 1827 3239
## IFNGR1 7484 3171 3176 2326 2015 4131
## TNFAIP3 16597 5208 1076 4672 5676 1445
## SOD2 42566 24016 35092 36778 25446 58887
## LPAL2 13 9 5 14 25 7
## PLG 0 1 0 0 1 0
## CCR6 20 10 183 102 118 90
## RAC1 2853 2539 3043 2609 2500 2890
## ZNF316 688 775 449 732 537 666
## AHR 791 744 1187 1197 1044 656
## IL6 0 1 1 1 9 2
## TOMM7 1057 1042 2065 2055 3559 1996
## CYCS 341 280 650 522 755 519
## AQP1 6 5 5 2 3 4
## NT5C3A 813 1083 776 657 737 728
## EGFR 0 1 0 0 0 0
## CD36 1159 1679 4106 2086 1523 2597
## SAMD9 1603 3799 2096 2017 1450 1643
## SERPINE1 8 3 14 8 8 3
## CUX1 1591 2001 1779 1797 1372 1640
## PSMC2 157 286 537 400 517 333
## NAMPT 88473 40641 34419 34555 30871 78661
## HYAL4 0 0 0 0 0 0
## LEP 4 1 3 2 0 4
## CALD1 11 9 12 6 12 16
## BRAF 795 727 663 594 601 683
## EZH2 34 40 44 42 91 72
## DNAJB6 1694 1337 1351 1569 1306 1718
## CSMD1 7 1 0 32 0 0
## CTSB 5371 6957 9075 5977 5427 5628
## EGR3 680 373 407 885 449 1046
## TNFRSF10A 51 55 204 139 185 146
## BNIP3L 2918 2111 2217 1736 1790 2631
## DUSP4 9 20 30 83 93 12
## NRG1 19 31 172 270 82 115
## RPL7 4395 3271 9731 8948 14529 10305
## IL7 1 6 18 12 14 12
## GEM 0 0 1 0 1 1
## MYC 196 141 897 837 1259 847
## GPT 1 0 3 2 5 0
## JAK2 1294 1476 1881 909 870 1115
## CD274 98 128 254 269 88 140
## IL33 0 0 0 0 0 0
## LURAP1L-AS1 0 0 0 0 0 0
## LURAP1L 2 2 0 2 2 2
## TTC39B 79 47 165 122 238 121
## IFNA1 0 0 0 0 0 0
## TEK 14 29 4 11 1 13
## TRBV20OR9-2 0 0 0 0 0 0
## TOMM5 109 120 286 253 325 216
## ANXA1 4865 8301 8502 10038 7984 6104
## ERP44 1252 1579 1497 1332 1160 1336
## ZNF483 12 6 23 29 30 15
## TNFSF15 2 13 6 4 1 7
## TLR4 10484 10469 7541 5027 3732 11464
## PTGS1 541 638 726 582 485 879
## HSPA5 5893 4080 3925 5313 5362 5102
## FNBP1 3136 3112 4009 3823 4451 3414
## CARD9 132 201 253 163 103 122
## TRAF2 63 62 148 128 136 104
## CLIC3 141 242 45 307 185 30
## IL2RA 49 40 123 89 188 76
## GATA3 88 89 435 358 492 217
## VIM 16412 17053 19366 21548 14994 15331
## CREM 156 90 126 224 254 155
## DKK1 0 0 0 0 0 1
## MBL2 0 0 0 0 0 0
## SAR1A 719 546 908 750 790 828
## PRF1 1796 3099 1234 7022 4840 1028
## ZMIZ1 2048 1907 1820 2407 1708 1570
## IFIT3 3365 35361 4510 6451 3393 1942
## TALDO1 12923 9946 8879 8401 5396 12138
## IGF2 1 0 0 1 0 0
## INS-IGF2 1 0 0 1 0 0
## IGF2-AS 0 0 0 0 0 0
## INS 0 0 0 0 0 0
## STIM1 980 1257 1545 1547 1649 1196
## TRIM22 3407 8639 4264 2780 2761 2003
## PTH 0 0 0 0 0 0
## SAA1 0 0 0 0 0 0
## SLC1A2 0 1 1 2 0 0
## FOSL1 31 48 14 107 48 36
## CCND1 0 3 3 10 10 5
## JRKL 44 44 113 60 103 76
## MMP7 0 0 0 0 1 0
## MMP1 0 2 1 0 0 0
## MMP3 0 0 0 0 0 0
## CASP1 2949 4349 4242 3269 2311 3224
## DLAT 83 91 256 194 295 189
## IL18 131 87 137 88 65 67
## CD3E 908 583 3022 3420 6781 3028
## MCAM 275 209 245 194 227 304
## WNK1 3470 2952 4211 3785 3520 3602
## TNFRSF1A 4526 3507 4349 3187 2001 5191
## GAPDH 17522 16269 18227 21902 16022 23142
## CD4 1466 2207 5562 4465 5175 3093
## SLC2A3 10293 11010 6890 8050 6460 12909
## CLEC4D 1220 1814 559 217 209 868
## KLRB1 556 421 503 1119 1573 943
## CD69 1663 798 307 1134 2035 584
## CLEC2B 1621 918 1311 1391 1366 2124
## OLR1 64 53 5 15 13 56
## ABCD2 43 21 228 160 276 171
## LRRK2 19093 12876 9806 6842 3378 7781
## VDR 434 433 518 455 175 564
## TMBIM6 15329 12289 15005 13918 13063 16753
## PFDN5 1941 1887 3580 3549 4531 3907
## SP7 0 0 0 0 0 0
## MUCL1 0 0 0 0 0 0
## CD63 3648 3521 2567 3103 2318 3515
## SUOX 1276 971 1111 1042 874 1156
## RPS26 2594 490 3303 864 5713 3769
## RPL41 3794 4045 7688 7636 11972 8130
## IL23A 7 20 42 34 48 35
## DDIT3 888 622 190 319 323 459
## IFNG 29 28 7 17 16 4
## IL22 0 0 0 0 1 0
## LYZ 88414 86221 120660 51424 39935 77249
## CAPS2 5 2 2 7 4 1
## SYT1 1 0 6 3 1 5
## BTG1 13415 8912 7388 9368 8774 7835
## HCAR3 3210 1679 1938 2135 1015 5681
## GJB2 1 1 1 1 0 1
## GJB6 14 27 4 9 8 18
## TNFSF11 1 2 1 9 5 3
## TPT1 33863 25691 58601 47915 84417 69274
## LMO7 32 10 80 50 124 80
## TNFSF13B 1998 2554 2713 2296 1632 2582
## LAMP1 2643 2556 2860 3019 2733 3154
## PSME2 810 1549 2344 1847 1743 989
## GZMB 502 1031 489 1933 2073 246
## RPL36AL 1407 1445 2218 1855 3292 2567
## PYGL 9621 7326 5558 3651 2531 10609
## HIF1A 2300 2214 1721 2068 1596 1956
## FOS 68457 73043 14299 19092 4655 9169
## JDP2 2074 2549 658 754 489 833
## NOXRED1 15 6 4 7 1 9
## SERPINA1 30893 25712 19541 21968 11291 27733
## CDC42BPB 157 223 352 209 225 186
## PLA2G4D 0 0 0 0 0 0
## TRIM69 7 9 19 16 15 17
## SLC51B 0 0 0 0 0 0
## SMAD3 200 301 657 875 949 505
## CYP1A1 0 0 0 1 0 3
## AKAP13 6400 6619 5618 5433 5040 4083
## MEFV 3397 3751 3362 2753 1421 2790
## SOCS1 153 207 47 112 67 31
## ATXN2L 1011 1226 1724 1798 2265 1643
## CD19 0 28 86 112 144 123
## ITGAL 4467 6187 5938 6858 7258 4374
## ITGAM 7037 7165 5991 5175 4034 7118
## ITGAX 7376 6287 3593 3748 2432 4603
## DNAJA2 711 646 878 503 683 805
## SIAH1 139 105 118 112 110 104
## ADCY7 2268 3234 3548 3371 2840 2239
## NOD2 796 505 768 794 426 967
## CMTM2 4903 2807 2323 1676 1327 3226
## SF3B3 391 539 1119 939 1243 805
## PSMD7 616 554 737 706 802 772
## WWOX 19 25 37 66 84 42
## MAF 120 207 519 701 608 291
## SLC7A5 222 133 179 302 380 251
## CXCL16 4630 2283 1720 2349 1576 1942
## XAF1 278 3640 1073 1254 1224 515
## CD68 2685 4076 6464 6077 3519 2898
## PER1 4536 3447 285 815 840 255
## NOS2 1 0 0 5 2 4
## TRAF4 18 36 58 101 143 61
## CCL2 0 3 38 33 27 10
## CCL5 1507 2172 2122 7491 9407 2270
## CCL3 980 300 90 99 53 32
## CCR7 202 85 1036 751 1221 1015
## STAT3 6857 5681 5382 4242 3455 5629
## SOST 0 0 0 0 0 0
## ITGA2B 346 424 322 246 191 509
## EFCAB13 11 8 22 32 34 19
## NPEPPS 1162 1011 1005 649 648 1083
## TBX21 265 386 139 760 869 136
## COL1A1 1 3 0 0 0 0
## MRPS23 88 83 273 165 231 182
## MIR21 8 11 4 6 2 7
## RPS6KB1 335 209 483 442 482 383
## ACE 4 5 78 38 64 26
## ERN1 2782 1062 1057 824 1697 975
## PRTN3 116 80 1 14 8 20
## PLIN5 169 187 76 54 49 102
## RETN 144 217 61 71 26 114
## CCL25 1 2 0 2 0 1
## ICAM1 1369 933 1334 1797 1164 1979
## TYK2 2124 2227 2002 1546 1346 1508
## SMARCA4 404 494 720 757 970 571
## ACP5 122 113 421 399 357 249
## JUNB 70681 30392 13303 24046 14982 15835
## CYP4F22 38 76 77 70 29 7
## JAK3 1468 1549 951 1257 1520 1792
## JUND 9421 11950 3254 7009 5254 3179
## CEBPA 666 1217 1222 831 576 934
## CEBPG 166 174 402 285 346 250
## ACP7 0 0 1 0 0 0
## ZFP36 74369 22579 8994 13532 7822 8026
## TGFB1 4607 6252 4611 5997 5667 4647
## RPS19 3909 4295 9712 10982 15308 10514
## PSG2 0 0 0 0 0 0
## FUT2 1 1 2 2 1 1
## NKG7 2510 3735 1254 8104 8982 1723
## ZNF415 1 13 8 26 2 6
## LILRB2 4806 5394 4486 5414 3218 4066
## LILRA5 2201 3560 2873 2932 2232 4543
## KIR3DL1 83 102 11 79 235 34
## KIR3DL2 36 35 12 34 100 19
## SMOX 81 54 73 84 76 141
## BMP2 20 7 10 2 1 13
## GINS1 5 8 11 7 13 9
## PLCG1 242 213 772 631 1268 786
## YWHAB 5288 5609 6709 5743 5854 6074
## PI3 652 291 686 1214 267 1624
## MMP9 7669 10488 3643 798 881 4171
## CD40 29 41 368 172 225 166
## PFDN4 22 16 59 45 44 45
## BMP7 0 0 0 0 0 0
## RPS21 1981 1683 4478 4620 7817 5268
## MX1 708 9716 1534 2241 1365 747
## PFKL 600 1079 1504 1390 1434 981
## IL17RA 8409 9432 7470 4696 3724 7315
## UBE2L3 818 918 1320 1123 1261 1185
## TPST2 1244 984 1020 1740 1556 1542
## XBP1 570 571 1267 1164 1892 1363
## UQCR10 413 458 643 635 672 587
## SEC14L2 11 2 19 25 45 30
## APOL6 954 2302 3193 2201 1373 955
## APOL1 443 863 1069 910 506 513
## TYMP 4112 8514 4399 4578 2917 2766
## BEND2 51 40 46 37 46 66
## PHEX 4 2 9 16 8 12
## TIMP1 2415 913 1633 2149 1628 2047
## FOXP3 21 26 81 71 128 64
## MSN 28453 26670 22267 25192 22331 26756
## PGK1 9045 7220 8274 7712 7290 10467
## LAMP2 10173 6322 6113 5420 4492 8174
## CD40LG 46 25 299 131 304 150
## IRAK1 1402 1367 1379 1642 1563 1159
## COX2 28929 32135 48513 45066 75172 50998
## GSM3308485 GSM3308486 GSM3308487 GSM3308488 GSM3308489 GSM3308490
## TNFRSF9 65 148 102 125 76 101
## ENO1 5887 7041 7128 7442 7057 6942
## PIK3CD 3682 5947 6731 7862 6434 6526
## PGD 3094 5208 6307 6748 3930 6563
## MTHFR 287 355 357 520 588 283
## TNFRSF1B 9568 14651 13382 13161 11511 16570
## PINK1 419 1001 975 927 651 943
## IFNLR1 58 37 74 76 74 25
## RUNX3 3007 3426 3642 2825 3007 2079
## SH3BGRL3 7503 10229 12007 10685 8874 10941
## CD52 3581 4328 4049 5967 5283 4267
## IFI6 775 785 1763 931 601 3242
## ZC3H12A 269 458 346 231 251 280
## UTP11 87 58 65 172 149 82
## JUN 2942 2647 4654 423 262 15498
## KANK4 0 0 0 0 0 0
## EFCAB7 17 26 26 28 36 21
## IL23R 4 7 1 2 2 6
## ADGRL2 0 0 2 0 0 0
## GBP3 145 142 185 48 257 265
## GBP1 357 305 1756 1205 1452 1146
## GBP5 1049 919 3888 2309 4222 2272
## TGFBR3 745 574 1015 416 627 295
## VCAM1 1 3 0 3 4 0
## PTPN22 306 335 326 478 586 278
## CD160 117 55 57 102 101 54
## FCGR1A 404 549 1972 566 824 618
## MCL1 10759 21457 22508 21067 18814 37507
## CTSK 28 34 21 28 46 43
## RORC 81 50 30 142 292 93
## S100A9 70185 116062 139233 99934 59565 165127
## S100A12 2757 5398 3782 3491 1653 5023
## S100A8 25996 45142 52973 34443 23975 61638
## IL6R 2736 3745 5548 5901 5050 4283
## RIT1 834 1508 1289 1269 935 1583
## BGLAP 4 8 8 12 4 8
## IFI16 1506 2366 3930 3805 3628 3380
## AIM2 74 121 142 115 199 201
## CRP 0 0 0 0 0 0
## FCGR2A 5756 12250 15841 15563 10396 12725
## HSPA6 715 1677 1836 2327 2084 1966
## FCGR3A 7690 13576 19482 18513 15076 12386
## SELL 19602 24473 36293 31577 23058 55215
## GLUL 8182 16836 14654 11588 8989 13120
## PTGS2 872 3025 5826 11417 7152 9915
## CRB1 1 1 1 2 2 1
## KDM5B 258 470 319 577 529 488
## IL10 5 2 1 1 2 23
## YOD1 182 232 125 117 189 277
## HHAT 36 39 30 30 39 31
## TRAF5 280 270 195 427 505 230
## NLRP3 483 741 1010 805 495 1105
## LINC01250 0 0 0 2 0 0
## RPS7 9106 10264 7814 9777 10012 7499
## RSAD2 172 235 824 372 334 2798
## FOSL2 2094 3498 3033 2758 2211 3196
## REL 870 1053 789 1344 1250 971
## TGFA 330 536 493 570 425 671
## DYSF 2411 5687 5956 4871 3530 6398
## HK2 455 1100 664 1785 846 1826
## CD8A 1173 1603 2790 864 1536 598
## CD8B 629 1079 874 427 757 360
## EIF5B 399 427 424 678 812 494
## IL1R1 168 381 210 151 178 319
## RGPD6 67 66 45 82 125 48
## IL1A 1 0 0 0 0 1
## IL1B 131 256 654 1566 877 324
## IL37 0 0 0 0 0 0
## IL36RN 0 0 0 0 0 0
## IL1F10 0 0 0 0 0 0
## IL1RN 1416 2450 3335 2092 1457 2024
## NMI 983 1155 1844 1325 1233 2152
## TNFAIP6 217 353 624 333 191 878
## IFIH1 191 258 394 438 519 575
## SCN1A 0 0 0 0 0 0
## ABCB11 1 1 2 0 1 0
## RBM45 47 44 38 67 72 58
## FRZB 0 0 0 2 0 0
## TFPI 3 3 5 13 9 2
## STAT1 2262 2775 6089 5592 4613 3716
## NABP1 233 380 444 430 479 756
## SF3B1 2974 4255 4102 3939 4376 4244
## CASP10 226 270 331 444 477 378
## CD28 621 663 257 614 1083 589
## CTLA4 46 54 17 41 63 60
## ICOS 150 186 80 146 258 103
## NDUFS1 367 489 492 746 608 493
## CXCR2 8019 21603 24490 29096 19924 25966
## IRS1 78 143 81 107 92 60
## CCL20 1 0 0 1 4 2
## ATG16L1 231 215 179 280 306 211
## GPR35 101 70 116 58 87 92
## PDCD1 36 26 20 68 71 52
## PPARG 4 4 8 5 8 7
## RPL15 14362 17061 12934 17263 17507 11741
## EOMES 111 117 119 201 248 65
## CX3CR1 576 397 1556 2350 2099 1002
## ACKR2 1 0 0 3 0 0
## CCR2 778 754 823 1592 1805 1763
## CCRL2 24 21 42 46 32 49
## TLR9 46 81 80 132 132 62
## ARHGEF3 819 750 821 1021 1302 741
## ADAMTS9 0 0 0 0 0 0
## TMEM45A 3 0 3 3 2 2
## CD80 7 7 4 8 9 7
## CD86 795 1018 1079 1010 940 1104
## MIX23 19 23 38 36 50 12
## PLS1 15 42 29 14 19 21
## PTX3 47 52 82 30 32 27
## GOLIM4 87 56 73 136 144 84
## MYNN 193 259 301 330 328 268
## TNFSF10 1217 1869 4331 3823 3569 4584
## ADIPOQ 0 0 0 0 0 0
## SPON2 250 86 329 600 182 327
## S100P 2244 3581 4724 2811 149 2303
## WDR1 4135 5468 6449 6970 6606 5877
## CD38 173 109 157 395 165 168
## PPARGC1A 2 16 2 5 5 5
## TMPRSS11B 0 0 0 0 0 0
## CSN3 0 0 0 0 0 0
## ALB 0 2 0 0 0 0
## CXCL8 11559 26568 24013 10986 3621 35418
## CXCL2 1 8 13 2 4 14
## AREG 35 39 30 6 3 224
## CXCL10 21 13 45 42 24 11
## CXCL13 0 0 0 1 0 0
## SPP1 52 18 195 150 24 33
## HERC6 143 139 170 220 239 259
## NFKB1 686 959 774 1451 1423 945
## SEC24B 322 490 392 567 630 464
## EGF 23 24 41 47 52 18
## IL2 1 1 1 1 2 0
## IL21 0 0 1 2 0 4
## IL21-AS1 0 0 5 0 1 1
## SLC7A11 12 12 16 13 13 14
## IL15 41 54 79 86 90 74
## EDNRA 0 0 0 0 0 0
## TLR2 2264 4074 5399 3937 3624 7317
## FGB 0 0 0 0 0 0
## DDX60 227 203 350 430 507 829
## SPCS3 1748 1800 1898 2520 2519 2030
## TLR3 8 7 9 18 21 2
## OSMR 17 32 21 19 18 34
## GZMK 1192 656 221 367 872 464
## GZMA 1211 854 1542 825 966 624
## ANKRD55 34 158 25 66 111 101
## CENPK 73 66 37 48 88 77
## CAST 2538 2413 2949 3055 2797 2592
## ERAP1 1627 1169 1274 2176 2563 1157
## ERAP2 1394 1538 2880 1637 1998 170
## TNFAIP8 1287 1519 995 1962 2296 1233
## CSF2 0 0 0 1 2 0
## IL5 1 0 0 0 1 0
## IL13 0 0 0 0 0 0
## IL4 3 4 2 10 4 0
## CD14 8037 12600 9188 7750 5544 10297
## CSNK1A1 1048 1473 1356 2549 2507 1834
## PPARGC1B 79 92 83 67 103 119
## TNIP1 2932 4380 3945 4082 3548 5836
## ATOX1 123 159 220 217 147 228
## FAXDC2 113 180 162 260 265 108
## IL12B 1 1 2 0 1 1
## MIR146A 0 0 0 0 0 0
## PDLIM7 866 1713 1732 1433 889 2125
## SERPINB1 2875 4220 5951 5173 3782 5361
## SSR1 1926 2436 2321 2588 2678 2571
## CD83 408 314 591 255 160 144
## SOX4 177 133 133 170 144 217
## CMAHP 71 63 80 80 85 101
## HLA-A 32322 43467 61777 46083 39190 51486
## HLA-C 40753 46205 98016 80980 53425 118637
## HLA-B 55318 106560 113999 103173 85372 103510
## MICA 94 100 135 127 123 131
## LTA 57 56 60 119 100 65
## TNF 179 154 233 162 199 21
## HLA-DRB1 3120 6037 4973 5564 3131 3743
## HLA-DQB1 566 1473 4485 1607 488 238
## PPARD 252 405 221 407 479 283
## CCND3 3364 5290 4733 4578 5368 6124
## VEGFA 126 157 155 112 125 250
## RUNX2 454 772 332 452 425 496
## IL17A 0 0 0 0 0 0
## IL17F 0 0 0 2 0 0
## PRDM1 441 593 673 767 887 1203
## ATG5 349 380 359 445 508 347
## TRAF3IP2 169 277 165 207 274 196
## NCOA7 353 296 381 475 544 377
## SGK1 1421 2326 2777 4163 2959 1497
## IFNGR1 1803 2971 3243 4128 3441 4741
## TNFAIP3 3048 3343 2126 820 1067 7119
## SOD2 21349 37490 48427 45203 28540 29308
## LPAL2 8 10 9 10 15 6
## PLG 0 0 0 0 0 0
## CCR6 134 91 64 463 436 72
## RAC1 1942 3190 3858 3750 2926 2711
## ZNF316 477 676 729 551 513 791
## AHR 981 770 845 682 629 889
## IL6 5 4 1 5 6 3
## TOMM7 2124 3212 1834 2459 2946 1848
## CYCS 538 417 525 628 690 609
## AQP1 0 4 6 1 0 0
## NT5C3A 430 691 871 768 710 854
## EGFR 0 0 0 0 0 0
## CD36 2124 1702 3819 2281 1875 3548
## SAMD9 944 1163 1906 1779 1791 2919
## SERPINE1 6 6 8 17 24 3
## CUX1 1138 1632 1550 1297 1432 1632
## PSMC2 282 289 349 587 558 337
## NAMPT 26973 55338 48800 38327 29914 54807
## HYAL4 1 0 0 0 0 0
## LEP 2 1 1 5 5 3
## CALD1 14 8 24 16 35 4
## BRAF 468 760 564 674 704 780
## EZH2 43 46 49 57 74 53
## DNAJB6 953 1426 1635 1544 1436 1442
## CSMD1 0 2 0 2 5 0
## CTSB 5502 5470 8118 6760 6432 7557
## EGR3 263 261 974 395 166 268
## TNFRSF10A 143 140 99 159 219 124
## BNIP3L 1443 2070 2171 2572 2092 2252
## DUSP4 35 56 20 21 36 54
## NRG1 96 204 121 35 52 399
## RPL7 10430 13251 8235 10944 13134 8300
## IL7 22 12 26 42 38 7
## GEM 0 0 1 2 4 0
## MYC 695 1332 697 1098 1511 984
## GPT 1 0 2 2 0 1
## JAK2 582 757 1189 1134 1040 1245
## CD274 73 161 416 158 197 82
## IL33 1 0 0 0 0 0
## LURAP1L-AS1 0 0 0 0 0 0
## LURAP1L 0 0 0 2 3 0
## TTC39B 136 150 130 133 203 138
## IFNA1 0 0 0 0 0 0
## TEK 2 11 18 18 37 5
## TRBV20OR9-2 0 1 0 0 0 0
## TOMM5 246 196 222 275 272 196
## ANXA1 5461 5870 11230 6474 6473 6464
## ERP44 967 1254 1467 1292 1101 1555
## ZNF483 30 23 9 27 53 30
## TNFSF15 1 3 3 4 7 7
## TLR4 3140 6232 7182 5640 5244 12584
## PTGS1 610 603 881 1138 897 580
## HSPA5 4068 6020 5896 5129 4514 5567
## FNBP1 2997 3936 3435 4474 4551 3265
## CARD9 131 104 132 150 126 193
## TRAF2 90 110 98 167 180 96
## CLIC3 79 37 92 126 77 105
## IL2RA 92 94 61 152 213 169
## GATA3 271 259 207 420 589 243
## VIM 13448 22450 24980 16982 15521 21364
## CREM 129 148 109 130 101 186
## DKK1 0 0 0 0 0 0
## MBL2 0 0 0 0 1 0
## SAR1A 535 696 740 910 903 693
## PRF1 1394 1159 3219 2769 2179 1392
## ZMIZ1 1523 2446 2271 2441 1894 2509
## IFIT3 1436 1869 6619 2807 2833 11579
## TALDO1 5170 9801 10800 11678 6744 9385
## IGF2 0 0 0 0 0 1
## INS-IGF2 0 0 0 0 0 1
## IGF2-AS 0 0 0 0 0 0
## INS 0 0 0 0 0 0
## STIM1 998 1531 1356 1669 1642 1324
## TRIM22 1413 1743 3502 3258 3907 4436
## PTH 0 0 0 0 0 0
## SAA1 0 0 0 0 0 0
## SLC1A2 0 3 0 0 1 0
## FOSL1 14 38 49 11 5 19
## CCND1 6 6 6 10 4 6
## JRKL 63 62 57 132 162 88
## MMP7 0 0 0 0 0 0
## MMP1 0 2 8 0 6 0
## MMP3 0 0 0 0 0 0
## CASP1 1779 2300 3452 2743 2429 2718
## DLAT 183 186 176 263 299 151
## IL18 100 95 152 85 92 122
## CD3E 3471 3989 2759 2563 4635 3129
## MCAM 170 248 214 211 283 206
## WNK1 2507 4730 3411 4896 5009 4940
## TNFRSF1A 1858 3566 5020 5579 3947 4121
## GAPDH 14132 18924 21154 18008 14885 20405
## CD4 3948 4800 3539 3724 4508 5116
## SLC2A3 4524 10173 9664 5503 4165 6624
## CLEC4D 220 473 565 295 299 608
## KLRB1 1292 735 554 1199 1114 688
## CD69 938 788 698 386 372 1847
## CLEC2B 939 1612 2020 1166 1289 1930
## OLR1 4 14 154 22 53 14
## ABCD2 154 188 105 169 303 152
## LRRK2 4795 6463 7395 6768 6250 7279
## VDR 228 440 394 446 422 471
## TMBIM6 8699 13919 15304 15664 13709 14319
## PFDN5 3041 3811 3193 3485 3647 2960
## SP7 0 0 0 0 0 0
## MUCL1 0 0 0 0 0 0
## CD63 1776 3391 3707 2806 2157 3478
## SUOX 714 1077 1152 1318 1098 1159
## RPS26 3587 743 3119 836 4380 2905
## RPL41 7670 9780 7037 8967 9148 7468
## IL23A 35 41 12 46 76 31
## DDIT3 239 458 423 249 219 278
## IFNG 7 9 38 8 14 3
## IL22 0 1 0 0 0 0
## LYZ 79371 97990 102698 68481 32333 117457
## CAPS2 4 4 4 8 4 4
## SYT1 0 3 7 6 3 8
## BTG1 6114 10290 7997 8504 8283 14502
## HCAR3 1043 1842 4043 2205 1560 1350
## GJB2 0 0 0 0 0 0
## GJB6 4 9 11 4 6 5
## TNFSF11 2 2 1 2 8 1
## TPT1 59404 65625 49532 56599 65120 49163
## LMO7 47 84 47 101 154 64
## TNFSF13B 1373 1983 2561 2073 1679 3296
## LAMP1 2132 2880 3051 2730 2685 3157
## PSME2 982 857 1548 1385 1260 1138
## GZMB 398 593 1402 997 556 557
## RPL36AL 2167 2918 2097 2066 1959 2494
## PYGL 3023 5322 6486 5397 3252 4874
## HIF1A 1302 2488 1483 2455 1744 2466
## FOS 14735 24711 31575 16107 11384 105817
## JDP2 386 756 781 597 462 2003
## NOXRED1 7 8 1 4 5 13
## SERPINA1 15407 27008 24775 21378 13924 30699
## CDC42BPB 160 255 233 224 247 246
## PLA2G4D 0 0 0 0 0 0
## TRIM69 7 21 14 11 19 25
## SLC51B 0 0 0 0 2 0
## SMAD3 635 578 516 759 756 490
## CYP1A1 0 3 0 1 0 0
## AKAP13 3305 4318 4858 5123 5809 4791
## MEFV 1342 2555 3044 3405 2470 3646
## SOCS1 43 77 60 41 28 225
## ATXN2L 1485 1846 1366 1738 1907 1757
## CD19 119 137 125 582 273 68
## ITGAL 3440 4618 5544 5837 6117 5105
## ITGAM 3807 4792 6592 5420 4159 6320
## ITGAX 2785 5581 3256 4072 3099 3731
## DNAJA2 441 564 569 886 868 745
## SIAH1 89 114 85 192 191 88
## ADCY7 1883 2192 2521 2359 2849 2699
## NOD2 213 840 1008 932 472 554
## CMTM2 1235 1871 2186 2187 1479 2868
## SF3B3 665 795 796 1123 1401 858
## PSMD7 599 660 655 804 811 576
## WWOX 39 44 34 51 39 49
## MAF 447 279 390 627 685 516
## SLC7A5 275 250 156 204 227 214
## CXCL16 1108 2246 1855 1489 1215 2345
## XAF1 573 481 1043 664 669 1834
## CD68 3167 4246 4773 4026 3564 5101
## PER1 557 712 564 223 386 2356
## NOS2 3 1 0 0 1 1
## TRAF4 95 90 52 140 131 63
## CCL2 12 8 21 21 9 0
## CCL5 3618 3741 5033 2762 3319 1367
## CCL3 39 75 139 201 112 118
## CCR7 710 1287 378 1447 2659 850
## STAT3 2490 4611 5718 6229 4973 5567
## SOST 0 0 0 0 0 0
## ITGA2B 306 526 757 901 583 271
## EFCAB13 25 25 15 34 28 21
## NPEPPS 526 846 893 1017 963 919
## TBX21 245 177 460 347 326 153
## COL1A1 1 0 0 0 0 3
## MRPS23 137 118 191 301 273 161
## MIR21 3 10 3 8 6 3
## RPS6KB1 323 378 282 373 560 360
## ACE 63 24 30 47 89 43
## ERN1 1194 1220 799 899 1529 1406
## PRTN3 8 18 228 23 5 6
## PLIN5 32 69 73 101 53 87
## RETN 54 61 231 48 56 75
## CCL25 0 1 0 0 0 1
## ICAM1 796 1442 1463 989 677 823
## TYK2 941 1373 1571 2017 1668 2028
## SMARCA4 641 697 575 767 925 778
## ACP5 218 245 215 608 389 271
## JUNB 15090 21623 32473 14105 8480 23179
## CYP4F22 19 27 106 22 35 13
## JAK3 968 1519 1169 1356 1442 1719
## JUND 4256 5174 8092 3640 2418 10600
## CEBPA 647 1032 1174 806 682 774
## CEBPG 238 218 271 354 423 258
## ACP7 0 0 0 0 0 1
## ZFP36 7073 12623 25128 13491 9928 18281
## TGFB1 4272 5579 5830 5245 3871 5257
## RPS19 10148 12296 9469 12262 11726 8689
## PSG2 0 0 0 0 0 0
## FUT2 1 4 3 4 2 3
## NKG7 2742 2162 6241 3094 2558 1455
## ZNF415 4 8 7 6 8 1
## LILRB2 2612 4073 3944 3733 3631 4757
## LILRA5 1721 2682 2731 2489 2634 2808
## KIR3DL1 48 83 64 82 43 48
## KIR3DL2 42 44 126 35 31 20
## SMOX 83 101 162 191 97 59
## BMP2 3 13 4 4 10 4
## GINS1 4 5 12 12 12 12
## PLCG1 738 821 448 658 1384 741
## YWHAB 4695 5740 6504 7004 6585 6082
## PI3 216 3779 952 1450 645 631
## MMP9 1803 3463 3428 2125 888 4808
## CD40 156 170 194 384 290 161
## PFDN4 38 35 37 64 52 51
## BMP7 0 0 0 0 0 0
## RPS21 5088 6120 4242 5604 6202 4197
## MX1 598 1003 1143 1291 1188 3351
## PFKL 995 1171 1210 1486 1482 1078
## IL17RA 3175 5869 6553 6543 5642 7414
## UBE2L3 759 1144 1110 1374 1386 1083
## TPST2 823 1129 1622 1238 1013 1103
## XBP1 1117 1173 974 1353 1565 964
## UQCR10 452 518 593 717 593 634
## SEC14L2 45 53 12 18 35 34
## APOL6 776 846 2343 1731 2296 1326
## APOL1 343 282 890 567 544 566
## TYMP 2180 2646 4719 2349 2233 5911
## BEND2 35 34 61 87 85 10
## PHEX 9 9 16 27 18 12
## TIMP1 985 1880 1428 1928 1533 2192
## FOXP3 49 61 22 86 84 67
## MSN 16709 28453 26869 27398 22862 25207
## PGK1 5680 7930 8389 8331 7247 7350
## LAMP2 4274 7682 7847 7075 5485 8542
## CD40LG 198 164 109 272 486 173
## IRAK1 1291 1302 1506 1414 1376 1261
## COX2 62229 53770 62506 67663 59156 56414
## GSM3308491 GSM3308492 GSM3308493 GSM3308494 GSM3308495 GSM3308496
## TNFRSF9 114 178 128 151 196 280
## ENO1 6728 5352 6845 8204 3874 5599
## PIK3CD 5532 7369 4921 6307 10881 6087
## PGD 4547 6165 3949 4296 9483 5103
## MTHFR 410 313 359 425 317 346
## TNFRSF1B 11400 17180 14738 16557 11534 13822
## PINK1 650 921 630 737 1183 735
## IFNLR1 84 50 45 78 44 28
## RUNX3 3369 2572 3742 4824 2197 2667
## SH3BGRL3 9111 9753 11323 13039 9121 8908
## CD52 5432 3302 5889 5227 1546 3581
## IFI6 4073 2685 3091 1105 917 682
## ZC3H12A 739 369 509 445 246 280
## UTP11 95 102 81 89 69 104
## JUN 15628 2833 3709 5286 155 673
## KANK4 0 0 1 0 0 0
## EFCAB7 22 20 20 28 43 30
## IL23R 2 1 2 3 2 1
## ADGRL2 0 0 0 0 0 0
## GBP3 132 140 223 129 90 123
## GBP1 855 661 966 635 1014 900
## GBP5 2362 1426 3339 1562 1806 1801
## TGFBR3 390 435 514 1080 432 510
## VCAM1 0 0 1 8 2 1
## PTPN22 294 292 255 380 315 371
## CD160 106 23 114 203 32 148
## FCGR1A 744 524 651 610 2188 707
## MCL1 19287 26363 17200 20027 34505 15398
## CTSK 59 33 58 47 25 34
## RORC 53 53 50 64 78 37
## S100A9 102839 130843 84400 109831 183422 125884
## S100A12 2218 3978 1814 2791 5132 4590
## S100A8 40067 55195 31108 41140 85571 59504
## IL6R 2660 6009 3014 4650 8606 5047
## RIT1 1081 1230 1216 1358 1632 1076
## BGLAP 6 5 6 4 8 11
## IFI16 3013 3684 2695 2987 9522 3398
## AIM2 168 110 110 76 438 106
## CRP 0 0 0 0 0 0
## FCGR2A 12323 15166 10711 15200 28629 14692
## HSPA6 1451 1451 1434 1966 2780 1489
## FCGR3A 13763 18847 17796 17874 20546 15914
## SELL 28334 44916 36028 34436 47230 31730
## GLUL 11771 16552 13446 17052 15276 15148
## PTGS2 5680 6157 3265 5219 7823 4526
## CRB1 2 0 1 1 1 0
## KDM5B 377 434 343 436 553 378
## IL10 3 1 0 1 6 3
## YOD1 236 226 259 240 354 192
## HHAT 35 37 23 36 22 29
## TRAF5 411 219 253 320 196 238
## NLRP3 818 715 864 752 1436 498
## LINC01250 0 0 1 0 0 0
## RPS7 12925 7487 8507 10187 4311 7201
## RSAD2 1750 1177 1588 352 421 238
## FOSL2 3776 4480 3460 3851 6323 3159
## REL 1005 901 1018 1037 861 860
## TGFA 374 546 331 416 1388 482
## DYSF 5034 6893 3339 4324 10340 5808
## HK2 716 1282 897 1069 1603 1033
## CD8A 1519 1578 831 2759 561 547
## CD8B 1872 794 575 1156 256 266
## EIF5B 515 413 429 477 253 475
## IL1R1 202 285 141 243 739 203
## RGPD6 63 72 58 67 69 71
## IL1A 0 0 1 1 0 0
## IL1B 789 882 311 612 1326 537
## IL37 0 0 0 1 0 0
## IL36RN 0 0 0 0 0 0
## IL1F10 0 0 0 0 0 0
## IL1RN 5686 3217 2070 2618 3324 3041
## NMI 1314 1949 1517 1350 2274 1536
## TNFAIP6 1234 740 222 741 923 353
## IFIH1 633 426 512 358 183 269
## SCN1A 0 0 0 0 0 0
## ABCB11 0 1 2 0 5 1
## RBM45 55 54 45 56 36 54
## FRZB 0 0 0 2 0 0
## TFPI 0 3 7 1 6 2
## STAT1 4113 4348 4979 4163 3338 3615
## NABP1 465 677 403 625 1473 531
## SF3B1 3561 4114 3701 4185 4783 4176
## CASP10 299 257 338 309 288 235
## CD28 747 583 625 679 285 486
## CTLA4 65 66 81 66 52 47
## ICOS 215 165 149 144 90 150
## NDUFS1 400 547 499 595 434 545
## CXCR2 10511 26024 13514 27018 54251 20350
## IRS1 193 89 95 72 82 90
## CCL20 1 2 3 1 3 0
## ATG16L1 318 217 247 287 201 225
## GPR35 115 76 134 123 30 104
## PDCD1 22 40 16 62 25 8
## PPARG 1 2 3 2 5 6
## RPL15 21925 12226 14065 17227 6609 11628
## EOMES 33 43 70 268 134 85
## CX3CR1 638 779 1020 1763 930 1373
## ACKR2 1 1 1 0 1 0
## CCR2 284 538 430 670 377 695
## CCRL2 37 24 20 21 50 33
## TLR9 46 57 48 71 95 62
## ARHGEF3 1157 789 1188 1270 556 904
## ADAMTS9 0 0 0 0 0 0
## TMEM45A 1 4 2 1 15 9
## CD80 4 5 7 8 0 0
## CD86 814 784 965 943 141 846
## MIX23 21 14 20 31 12 17
## PLS1 24 21 20 18 16 18
## PTX3 80 30 29 23 77 88
## GOLIM4 58 83 94 111 36 94
## MYNN 266 271 260 324 300 284
## TNFSF10 2554 3732 3061 3005 5318 2691
## ADIPOQ 0 0 0 0 0 0
## SPON2 390 159 581 981 627 511
## S100P 2630 2353 1961 1468 8501 1969
## WDR1 4535 6357 6082 6964 6937 6021
## CD38 297 136 333 317 155 219
## PPARGC1A 3 4 0 2 1 8
## TMPRSS11B 0 0 0 0 0 0
## CSN3 0 0 0 0 0 0
## ALB 2 0 0 0 0 0
## CXCL8 47185 18300 12140 30857 12756 9388
## CXCL2 8 6 7 8 6 3
## AREG 51 13 67 40 27 6
## CXCL10 52 15 18 20 1 23
## CXCL13 0 1 1 0 0 0
## SPP1 24 2 73 31 69 98
## HERC6 308 252 236 174 95 147
## NFKB1 853 845 867 1023 843 969
## SEC24B 369 408 423 519 408 384
## EGF 11 20 45 27 56 28
## IL2 0 1 0 2 0 0
## IL21 0 0 2 0 0 1
## IL21-AS1 0 0 1 0 0 0
## SLC7A11 10 9 9 10 23 6
## IL15 69 69 88 80 33 72
## EDNRA 0 0 0 0 0 0
## TLR2 3061 3928 2351 3664 23267 3296
## FGB 0 0 0 0 0 0
## DDX60 588 546 645 361 218 305
## SPCS3 1628 1886 1648 2223 1880 2257
## TLR3 2 3 8 20 3 13
## OSMR 16 36 39 28 29 21
## GZMK 348 212 637 1237 239 567
## GZMA 652 499 854 1817 809 951
## ANKRD55 65 80 33 71 73 75
## CENPK 29 51 84 90 35 56
## CAST 2284 2163 2714 3803 1560 3301
## ERAP1 896 1095 1336 1899 673 1398
## ERAP2 1629 105 1782 1667 856 2661
## TNFAIP8 1431 1455 1166 1592 1032 1159
## CSF2 1 1 0 0 0 1
## IL5 0 0 0 0 0 2
## IL13 0 1 0 0 0 0
## IL4 2 9 1 1 1 15
## CD14 9505 10349 7362 9094 10541 12260
## CSNK1A1 1254 1811 1392 1812 1793 1585
## PPARGC1B 132 102 183 116 33 88
## TNIP1 4457 5020 4041 4725 4018 4453
## ATOX1 195 163 178 195 116 160
## FAXDC2 109 113 198 171 229 143
## IL12B 0 0 0 1 1 0
## MIR146A 0 0 1 0 1 0
## PDLIM7 1293 1783 1370 1766 1795 1511
## SERPINB1 3751 4827 4122 5084 10371 4691
## SSR1 1792 2431 2189 2515 1793 2361
## CD83 741 298 407 256 45 569
## SOX4 181 138 294 236 40 151
## CMAHP 85 57 59 56 52 84
## HLA-A 41218 49804 47316 40709 39041 40021
## HLA-C 73116 116043 77740 83909 137823 87552
## HLA-B 103057 111782 99416 122512 117014 90833
## MICA 149 80 106 110 63 82
## LTA 92 55 62 66 44 42
## TNF 168 182 351 179 32 227
## HLA-DRB1 3555 3575 11700 5443 874 4662
## HLA-DQB1 3116 1142 7120 997 370 852
## PPARD 325 364 269 317 192 286
## CCND3 5069 3775 4254 5115 8234 3151
## VEGFA 156 135 245 137 58 123
## RUNX2 404 543 526 513 520 469
## IL17A 0 0 0 2 0 0
## IL17F 0 0 0 0 0 0
## PRDM1 269 586 436 749 973 402
## ATG5 307 335 386 408 281 344
## TRAF3IP2 243 187 168 246 149 170
## NCOA7 294 335 302 316 281 367
## SGK1 1974 2413 1414 1897 550 3748
## IFNGR1 1768 3050 2207 3699 8385 3042
## TNFAIP3 6664 1554 3033 2915 1727 1598
## SOD2 44677 62870 31629 46558 65865 45492
## LPAL2 11 5 11 12 6 13
## PLG 0 0 0 0 0 0
## CCR6 70 84 95 149 100 68
## RAC1 2183 3111 2820 3532 2966 2499
## ZNF316 653 574 805 832 264 624
## AHR 834 853 867 670 326 884
## IL6 9 3 2 3 2 2
## TOMM7 2811 2326 2362 2760 1149 1955
## CYCS 618 386 572 589 283 495
## AQP1 1 1 1 2 8 3
## NT5C3A 737 812 746 691 706 640
## EGFR 0 0 0 0 0 0
## CD36 1699 1947 2278 1659 387 2459
## SAMD9 1836 2489 1737 1699 2323 1630
## SERPINE1 6 6 17 8 47 9
## CUX1 1605 1603 1533 1437 1595 1556
## PSMC2 281 301 339 400 208 337
## NAMPT 44901 67492 35415 55157 95725 48109
## HYAL4 2 0 0 0 0 0
## LEP 3 6 0 4 3 6
## CALD1 5 12 32 14 37 18
## BRAF 611 727 569 585 806 576
## EZH2 68 42 38 66 56 43
## DNAJB6 1170 1538 1360 1687 1816 1300
## CSMD1 5 12 0 5 0 0
## CTSB 4785 5605 5911 6221 1741 5444
## EGR3 365 529 161 480 2193 857
## TNFRSF10A 191 114 143 133 89 132
## BNIP3L 1737 2751 1938 2353 2458 2362
## DUSP4 83 92 93 62 24 23
## NRG1 67 56 126 140 28 35
## RPL7 14783 9636 10228 11755 5108 8409
## IL7 15 18 10 19 7 9
## GEM 2 0 0 2 0 0
## MYC 503 1021 644 782 505 614
## GPT 2 1 2 1 0 2
## JAK2 796 947 902 871 1401 1055
## CD274 259 150 131 105 284 93
## IL33 0 0 0 0 0 0
## LURAP1L-AS1 0 0 0 0 0 0
## LURAP1L 1 1 2 2 1 3
## TTC39B 153 112 128 155 93 124
## IFNA1 0 0 0 0 0 0
## TEK 27 24 49 8 23 30
## TRBV20OR9-2 0 0 0 0 0 0
## TOMM5 241 209 217 250 108 205
## ANXA1 5345 5988 8072 5655 3808 5933
## ERP44 1166 1255 1365 1365 1102 1333
## ZNF483 23 28 37 38 15 30
## TNFSF15 2 12 5 3 3 8
## TLR4 3563 8042 3351 5092 10266 5767
## PTGS1 409 489 1070 754 994 622
## HSPA5 5661 3515 4449 5245 8320 5330
## FNBP1 3203 3767 3485 4141 2743 3248
## CARD9 164 116 189 199 48 175
## TRAF2 127 107 91 147 66 113
## CLIC3 108 40 111 218 119 86
## IL2RA 162 128 184 101 95 114
## GATA3 254 502 382 285 161 340
## VIM 15796 21782 19332 19336 9350 14897
## CREM 143 150 171 186 158 145
## DKK1 0 0 0 0 2 0
## MBL2 0 0 0 0 0 0
## SAR1A 604 779 754 841 699 671
## PRF1 1170 1335 2350 5814 2710 1764
## ZMIZ1 1763 2552 2890 2417 2069 2068
## IFIT3 11066 6249 7338 2509 3760 2257
## TALDO1 7565 10266 8153 11379 11910 8751
## IGF2 0 0 0 0 1 0
## INS-IGF2 0 0 0 0 1 0
## IGF2-AS 0 0 0 0 0 0
## INS 0 0 0 0 0 0
## STIM1 1302 1259 1203 1764 1234 1110
## TRIM22 2715 2666 3099 2377 5997 2072
## PTH 0 0 0 0 0 0
## SAA1 0 0 1 0 0 0
## SLC1A2 1 3 1 1 0 1
## FOSL1 34 64 38 2 15 25
## CCND1 8 1 4 7 9 7
## JRKL 71 80 58 89 66 80
## MMP7 0 0 0 0 0 0
## MMP1 0 0 0 1 1 1
## MMP3 0 0 0 0 0 0
## CASP1 2410 2901 2897 3128 4325 3182
## DLAT 167 171 166 224 97 162
## IL18 69 104 92 99 94 94
## CD3E 4674 3063 2671 4046 1320 2087
## MCAM 230 277 272 241 251 255
## WNK1 2968 4278 3321 4311 3406 4027
## TNFRSF1A 2523 4766 2641 4777 8800 3637
## GAPDH 19168 18282 15577 21054 11700 17992
## CD4 4157 3552 4573 4546 1085 4272
## SLC2A3 9897 14275 8390 7561 15719 9735
## CLEC4D 420 858 195 316 1835 404
## KLRB1 1012 385 997 1321 849 700
## CD69 2368 809 1261 1027 353 824
## CLEC2B 1376 2090 1572 1525 1552 1691
## OLR1 14 7 4 6 169 80
## ABCD2 209 184 160 205 100 156
## LRRK2 4923 8943 5011 6469 13084 7582
## VDR 254 465 372 443 393 417
## TMBIM6 11135 14678 11670 15340 16702 12810
## PFDN5 4537 3094 3349 4124 1776 3130
## SP7 0 2 0 0 0 0
## MUCL1 0 0 0 0 0 0
## CD63 2319 2499 2964 2879 3036 2740
## SUOX 811 1321 989 1255 1222 1113
## RPS26 5370 656 793 4178 455 5074
## RPL41 11320 7765 8213 9449 3897 7232
## IL23A 49 38 33 38 18 20
## DDIT3 461 319 452 370 630 394
## IFNG 23 4 15 31 4 4
## IL22 0 0 0 0 0 0
## LYZ 90993 37921 76361 64816 12163 53039
## CAPS2 2 5 3 9 3 1
## SYT1 4 2 1 0 1 2
## BTG1 10907 10167 9340 10745 7783 6858
## HCAR3 3420 2581 793 2535 7171 3763
## GJB2 3 3 0 0 0 0
## GJB6 15 12 14 11 13 13
## TNFSF11 0 7 2 6 0 5
## TPT1 81553 56267 59037 66597 34403 49019
## LMO7 97 56 44 70 52 84
## TNFSF13B 2783 2921 2330 2062 2567 1731
## LAMP1 2614 3042 2640 2940 2616 2434
## PSME2 1527 952 1893 1374 425 1119
## GZMB 723 476 936 1733 886 621
## RPL36AL 2813 2064 2534 2406 1449 1861
## PYGL 4371 6818 3588 5963 10972 6018
## HIF1A 1932 2035 2293 1964 2494 1644
## FOS 61601 25824 17911 25173 13787 8408
## JDP2 509 843 855 714 1429 703
## NOXRED1 6 8 5 6 26 6
## SERPINA1 21563 31132 26527 21980 38479 23307
## CDC42BPB 258 175 248 250 91 245
## PLA2G4D 0 0 0 0 0 0
## TRIM69 9 17 14 12 17 11
## SLC51B 0 0 0 0 0 0
## SMAD3 729 485 679 700 268 504
## CYP1A1 1 3 0 0 0 1
## AKAP13 3651 4231 3570 4594 8977 3893
## MEFV 2131 3689 2708 3427 4104 2761
## SOCS1 92 137 82 83 56 39
## ATXN2L 2247 1502 1619 1842 934 1315
## CD19 239 122 141 179 100 89
## ITGAL 4747 4449 5069 5924 3948 5029
## ITGAM 4475 5565 4342 4577 7539 5356
## ITGAX 4109 3336 4383 4663 4439 4167
## DNAJA2 555 607 513 660 618 594
## SIAH1 91 103 131 134 142 95
## ADCY7 2405 1858 2130 2618 1968 2423
## NOD2 818 892 751 706 1399 419
## CMTM2 1625 2645 1689 2214 4318 2543
## SF3B3 952 831 788 1114 493 766
## PSMD7 627 637 656 758 431 614
## WWOX 49 35 50 55 31 36
## MAF 477 530 922 525 341 396
## SLC7A5 248 214 210 268 261 163
## CXCL16 1667 2543 1912 1466 3205 1510
## XAF1 1575 1000 1535 693 354 586
## CD68 3609 3369 5302 3953 1190 3748
## PER1 840 436 764 648 1377 325
## NOS2 0 2 0 2 3 0
## TRAF4 137 64 96 81 33 52
## CCL2 29 19 1 7 2 15
## CCL5 2167 1863 2640 6581 2198 2203
## CCL3 251 66 104 273 44 77
## CCR7 1274 803 424 849 645 511
## STAT3 3273 5437 3743 5376 9643 4817
## SOST 0 0 0 0 0 0
## ITGA2B 164 199 466 373 689 336
## EFCAB13 33 16 18 17 16 23
## NPEPPS 620 994 650 925 1368 857
## TBX21 205 163 275 542 300 269
## COL1A1 0 1 1 0 1 0
## MRPS23 125 138 156 224 94 167
## MIR21 4 6 7 3 17 11
## RPS6KB1 353 343 318 403 333 360
## ACE 24 54 73 42 9 34
## ERN1 935 1128 934 1247 2069 652
## PRTN3 4 6 10 8 32 20
## PLIN5 85 104 59 92 301 58
## RETN 88 41 35 52 247 192
## CCL25 1 0 1 1 0 0
## ICAM1 2085 1366 1585 1588 949 1339
## TYK2 1223 1780 1303 1757 1835 1691
## SMARCA4 758 613 653 743 320 570
## ACP5 264 251 249 264 135 288
## JUNB 38070 32523 30507 28110 11137 16533
## CYP4F22 11 19 67 42 6 67
## JAK3 1771 1469 1224 1776 3033 1537
## JUND 13577 7980 7069 6051 3005 3258
## CEBPA 1056 925 1012 957 723 1028
## CEBPG 236 212 294 278 142 259
## ACP7 0 2 0 1 1 0
## ZFP36 32610 18711 17204 16607 7229 8528
## TGFB1 5180 5537 5745 5407 3221 3712
## RPS19 16606 9151 10954 11625 4983 9201
## PSG2 0 0 0 0 0 0
## FUT2 1 1 3 5 1 3
## NKG7 2441 1547 2993 7526 3657 2799
## ZNF415 3 8 5 5 9 8
## LILRB2 3874 3765 4620 4159 3372 4317
## LILRA5 1796 2337 2681 2083 2398 2455
## KIR3DL1 42 73 63 70 185 53
## KIR3DL2 15 20 57 48 93 35
## SMOX 66 78 109 117 214 93
## BMP2 4 5 5 2 8 10
## GINS1 11 7 4 18 5 7
## PLCG1 1077 613 632 804 526 677
## YWHAB 5078 6208 5516 6232 5366 5859
## PI3 1750 1390 1125 2356 256 1664
## MMP9 1445 4378 863 1661 7384 4667
## CD40 175 143 184 185 97 111
## PFDN4 55 53 45 57 29 49
## BMP7 0 0 0 0 0 0
## RPS21 8161 4925 5134 5964 2244 4335
## MX1 3559 2273 2765 1440 609 457
## PFKL 1263 1040 1306 1334 582 1032
## IL17RA 3822 7013 4511 5932 11676 5328
## UBE2L3 842 1024 1020 1243 846 949
## TPST2 1087 1047 1156 1460 1191 1024
## XBP1 862 852 1116 1251 917 1016
## UQCR10 556 514 574 682 412 507
## SEC14L2 78 29 15 36 13 21
## APOL6 1310 1258 1455 1275 1807 1339
## APOL1 567 587 845 553 538 591
## TYMP 4342 4196 4684 4328 1741 2725
## BEND2 16 27 39 79 120 56
## PHEX 4 17 5 13 6 20
## TIMP1 1438 2157 1880 2347 695 1310
## FOXP3 103 137 93 115 36 74
## MSN 20898 24097 24811 30794 24517 22761
## PGK1 7204 7378 7688 8618 9731 8209
## LAMP2 5130 8679 6047 7074 9561 7018
## CD40LG 130 207 134 207 114 149
## IRAK1 1504 1173 1552 1545 970 1200
## COX2 67325 44572 57346 77986 31634 41950
## GSM3308497 GSM3308498 GSM3308499 GSM3308500 GSM3308501 GSM3308502
## TNFRSF9 84 98 116 120 77 163
## ENO1 6223 6337 6559 5928 5945 5808
## PIK3CD 4545 7024 7566 9163 6008 6140
## PGD 3182 5495 5563 5988 4343 5736
## MTHFR 633 356 428 410 432 403
## TNFRSF1B 12067 11644 15568 14207 15320 15295
## PINK1 426 729 939 814 642 592
## IFNLR1 39 44 63 69 49 183
## RUNX3 2676 2341 3933 3226 3128 3490
## SH3BGRL3 8825 9496 10467 9566 10460 9885
## CD52 4714 4588 4323 3734 4942 3285
## IFI6 3668 931 676 650 546 5266
## ZC3H12A 1084 1133 511 355 575 605
## UTP11 47 48 114 132 70 76
## JUN 26857 20547 7995 425 831 452
## KANK4 0 0 0 0 0 0
## EFCAB7 21 20 35 31 25 25
## IL23R 0 4 0 1 9 0
## ADGRL2 0 0 0 0 0 0
## GBP3 392 193 160 277 215 344
## GBP1 2909 624 721 1117 805 5502
## GBP5 8742 1879 1683 2881 2619 16953
## TGFBR3 264 414 1153 1075 556 770
## VCAM1 1 2 6 5 2 1
## PTPN22 199 226 428 645 362 338
## CD160 45 92 85 161 130 46
## FCGR1A 2145 1071 729 372 1484 6900
## MCL1 29174 29729 20854 22808 17720 25655
## CTSK 89 56 50 39 51 51
## RORC 22 24 30 62 61 18
## S100A9 74654 183955 152129 122056 141519 191542
## S100A12 1541 6302 3344 3434 3239 3907
## S100A8 28075 75923 55500 50295 52054 78905
## IL6R 2745 4242 5010 6627 3422 3575
## RIT1 967 1355 1349 1288 1194 1336
## BGLAP 7 9 8 6 4 6
## IFI16 1904 2078 2700 3746 2821 6425
## AIM2 132 194 113 201 44 360
## CRP 0 0 0 0 0 0
## FCGR2A 8502 14723 14054 14657 15554 17777
## HSPA6 1031 1238 1437 5274 2200 2781
## FCGR3A 12948 16597 15728 23538 18625 23442
## SELL 30121 42607 37905 37742 24604 55456
## GLUL 14016 17207 20759 12462 18957 18304
## PTGS2 14686 21048 8237 7604 1840 1500
## CRB1 0 0 1 3 0 0
## KDM5B 416 473 437 603 418 404
## IL10 3 2 3 1 7 4
## YOD1 227 169 220 262 248 342
## HHAT 44 49 41 32 17 21
## TRAF5 350 324 377 415 483 282
## NLRP3 1626 1063 855 614 618 902
## LINC01250 0 0 1 0 2 0
## RPS7 9052 8416 8207 6533 12496 7501
## RSAD2 2695 332 151 238 83 7178
## FOSL2 3187 4228 4528 3216 2763 3204
## REL 987 934 1188 1276 1118 1171
## TGFA 299 530 521 721 441 689
## DYSF 3311 7138 5960 7420 4995 9095
## HK2 819 1127 980 1885 456 890
## CD8A 335 1005 930 2953 1134 1990
## CD8B 218 742 481 786 760 659
## EIF5B 398 454 587 602 430 427
## IL1R1 130 277 285 240 348 227
## RGPD6 50 42 92 101 92 49
## IL1A 23 6 0 1 2 0
## IL1B 6088 3296 848 1149 644 377
## IL37 0 0 0 0 0 0
## IL36RN 0 0 0 0 0 0
## IL1F10 0 0 0 0 0 0
## IL1RN 9938 11509 3120 2307 3214 4342
## NMI 1422 1360 1149 1482 1933 3066
## TNFAIP6 709 758 659 578 445 1291
## IFIH1 770 395 275 422 416 981
## SCN1A 0 0 0 0 0 0
## ABCB11 1 1 1 1 0 0
## RBM45 46 33 76 65 59 74
## FRZB 0 0 0 1 1 0
## TFPI 5 5 6 5 7 2
## STAT1 5677 2978 2938 4727 3008 11528
## NABP1 712 959 845 886 668 718
## SF3B1 4151 4842 4940 4604 4768 5402
## CASP10 405 276 329 433 327 405
## CD28 887 694 471 707 745 388
## CTLA4 130 54 70 70 134 92
## ICOS 203 135 124 201 494 217
## NDUFS1 348 339 535 644 416 522
## CXCR2 11020 16361 20346 23947 21010 19354
## IRS1 78 122 72 28 76 49
## CCL20 7 16 1 1 1 2
## ATG16L1 302 241 318 306 367 292
## GPR35 115 77 86 105 116 116
## PDCD1 16 33 51 108 25 50
## PPARG 1 4 0 7 4 8
## RPL15 15911 13315 12406 9962 16630 11180
## EOMES 55 118 128 487 126 109
## CX3CR1 531 797 1522 4250 841 951
## ACKR2 3 2 0 4 0 0
## CCR2 363 516 743 1610 517 612
## CCRL2 81 61 47 40 55 28
## TLR9 46 48 89 116 86 91
## ARHGEF3 1285 961 1047 1362 1149 1215
## ADAMTS9 0 0 0 0 1 0
## TMEM45A 2 7 4 2 0 2
## CD80 7 6 3 6 6 10
## CD86 1074 674 920 707 586 991
## MIX23 9 17 32 20 40 31
## PLS1 10 21 22 15 16 13
## PTX3 213 152 65 24 34 54
## GOLIM4 54 61 140 141 67 80
## MYNN 337 331 392 346 336 381
## TNFSF10 3005 2399 2334 4176 2407 5791
## ADIPOQ 0 0 0 0 0 0
## SPON2 397 182 437 382 244 354
## S100P 1022 4784 4430 3629 224 1586
## WDR1 4131 4748 6153 6722 5452 5839
## CD38 321 188 177 257 241 288
## PPARGC1A 2 8 3 4 2 0
## TMPRSS11B 0 0 0 0 0 0
## CSN3 0 0 0 0 0 0
## ALB 0 0 0 0 0 0
## CXCL8 69671 124095 56677 13508 7177 7053
## CXCL2 98 108 14 0 1 3
## AREG 143 106 27 0 17 76
## CXCL10 102 30 23 24 4 69
## CXCL13 0 0 0 2 1 0
## SPP1 20 20 67 40 123 25
## HERC6 249 157 162 218 190 283
## NFKB1 885 1037 915 1298 1212 989
## SEC24B 399 375 407 630 479 459
## EGF 37 48 29 46 42 22
## IL2 1 0 0 0 0 0
## IL21 1 3 0 2 1 0
## IL21-AS1 1 2 0 4 1 1
## SLC7A11 7 14 11 16 12 14
## IL15 118 78 96 83 60 100
## EDNRA 0 0 0 0 0 0
## TLR2 3174 4196 3679 4951 4251 7038
## FGB 0 0 0 0 0 0
## DDX60 688 236 277 520 225 1770
## SPCS3 1260 1626 2394 2425 1894 1834
## TLR3 5 6 14 42 2 14
## OSMR 25 20 29 29 27 46
## GZMK 270 694 652 875 838 332
## GZMA 452 730 1602 1517 1002 665
## ANKRD55 117 50 37 58 80 47
## CENPK 14 20 66 8 26 93
## CAST 2150 2126 4341 3180 2756 2334
## ERAP1 1413 1183 1677 2012 1600 1823
## ERAP2 1890 2241 1398 1743 1443 2202
## TNFAIP8 1217 1158 1509 1742 1564 1289
## CSF2 0 0 0 0 1 0
## IL5 0 0 0 0 0 0
## IL13 0 0 0 0 0 0
## IL4 2 3 6 2 0 0
## CD14 6626 10464 14154 7389 10472 12024
## CSNK1A1 1254 1341 1656 2204 1510 1741
## PPARGC1B 222 125 91 99 70 141
## TNIP1 3937 5094 4894 4463 5752 4593
## ATOX1 194 172 167 175 184 224
## FAXDC2 220 220 208 164 203 134
## IL12B 1 0 0 1 2 1
## MIR146A 0 0 0 0 0 0
## PDLIM7 1099 1864 1713 1749 2089 1840
## SERPINB1 3668 4851 4986 4644 5738 7715
## SSR1 1734 1704 2584 2141 1851 2290
## CD83 1343 1260 458 115 340 331
## SOX4 209 110 146 188 92 79
## CMAHP 98 76 87 107 172 127
## HLA-A 48295 33555 22870 40696 40182 45834
## HLA-C 51315 89602 73394 85009 84835 112204
## HLA-B 104537 104188 76822 74684 98411 153881
## MICA 168 167 123 152 45 86
## LTA 59 123 43 73 62 30
## TNF 233 225 415 168 189 199
## HLA-DRB1 8620 3181 3363 2549 3324 5223
## HLA-DQB1 4701 308 3186 269 2241 713
## PPARD 319 200 285 352 387 326
## CCND3 3848 3725 3943 3606 4341 5425
## VEGFA 220 202 99 122 97 105
## RUNX2 427 347 467 497 490 495
## IL17A 0 0 1 1 0 0
## IL17F 0 0 0 0 0 0
## PRDM1 637 289 461 1112 546 961
## ATG5 385 293 409 355 431 470
## TRAF3IP2 223 183 159 149 200 169
## NCOA7 339 283 364 405 283 532
## SGK1 4433 4428 2884 3845 4281 1689
## IFNGR1 1446 2038 3066 4256 3666 3515
## TNFAIP3 26895 20913 2206 1049 2462 4777
## SOD2 40590 57829 55811 40057 47013 68387
## LPAL2 11 17 22 42 24 14
## PLG 0 1 1 1 0 0
## CCR6 93 71 82 153 130 50
## RAC1 1678 2564 3028 2793 2967 2856
## ZNF316 992 777 783 729 982 638
## AHR 2635 932 1338 524 1149 1273
## IL6 21 14 5 0 6 0
## TOMM7 2035 1975 2367 1558 2638 1793
## CYCS 808 796 573 568 422 508
## AQP1 3 7 5 3 2 2
## NT5C3A 660 721 730 703 670 1303
## EGFR 0 0 0 0 0 0
## CD36 2881 2970 2042 1903 1729 1371
## SAMD9 2140 1502 1862 2015 1305 2999
## SERPINE1 21 21 27 15 17 5
## CUX1 1653 1655 1577 1457 1096 1464
## PSMC2 268 241 356 472 314 387
## NAMPT 42289 62601 56675 41178 67250 94769
## HYAL4 1 0 0 0 0 0
## LEP 0 1 1 16 1 3
## CALD1 21 52 21 9 22 11
## BRAF 593 666 713 765 636 598
## EZH2 70 73 58 67 69 68
## DNAJB6 1038 1195 1776 1274 1391 1430
## CSMD1 8 0 1 2 2 4
## CTSB 6091 4796 5292 4851 4968 5469
## EGR3 1345 1118 1764 109 922 822
## TNFRSF10A 165 161 142 167 191 154
## BNIP3L 1452 1559 2416 2158 2047 2046
## DUSP4 124 101 31 24 31 54
## NRG1 102 93 79 41 235 69
## RPL7 11367 9678 9122 7097 11744 7802
## IL7 9 12 18 14 24 24
## GEM 5 6 0 0 0 0
## MYC 264 302 545 632 1557 902
## GPT 5 1 0 3 1 1
## JAK2 1288 1212 1098 1479 767 1661
## CD274 609 232 103 175 334 1363
## IL33 0 0 0 0 1 0
## LURAP1L-AS1 0 0 0 0 0 0
## LURAP1L 1 2 5 2 7 0
## TTC39B 196 145 137 211 249 150
## IFNA1 0 0 0 0 0 0
## TEK 26 28 9 10 3 9
## TRBV20OR9-2 0 0 0 0 0 0
## TOMM5 197 224 262 227 203 242
## ANXA1 7085 5621 8016 5345 4941 7476
## ERP44 1353 1262 1564 1079 1055 1780
## ZNF483 40 28 27 57 21 24
## TNFSF15 4 7 5 11 1 4
## TLR4 3878 5176 8582 7123 5374 8334
## PTGS1 956 1051 785 760 1049 582
## HSPA5 6400 10367 8092 3571 5650 5519
## FNBP1 2133 2630 3573 3941 3312 3373
## CARD9 245 163 166 209 133 167
## TRAF2 129 102 125 148 150 116
## CLIC3 56 55 97 133 92 61
## IL2RA 132 78 127 89 118 140
## GATA3 343 286 313 396 294 171
## VIM 16362 17146 17569 15163 15268 14487
## CREM 182 128 210 140 195 249
## DKK1 0 1 0 0 0 0
## MBL2 0 0 0 0 0 0
## SAR1A 769 575 874 998 867 938
## PRF1 1125 387 3081 3467 1695 1920
## ZMIZ1 2234 1738 2186 2220 1915 2258
## IFIT3 15270 2849 1741 2704 1680 18101
## TALDO1 5787 8908 9105 9570 9430 9255
## IGF2 1 0 0 0 0 0
## INS-IGF2 1 0 0 0 0 0
## IGF2-AS 0 0 0 0 0 0
## INS 0 0 0 0 0 0
## STIM1 1000 1108 1311 1445 1364 1368
## TRIM22 3423 1868 1879 2015 1833 9534
## PTH 0 0 0 0 0 0
## SAA1 0 0 0 0 0 1
## SLC1A2 0 1 0 2 0 3
## FOSL1 118 161 82 3 36 33
## CCND1 10 8 4 7 12 10
## JRKL 63 82 72 148 83 48
## MMP7 0 0 0 0 0 0
## MMP1 3 0 3 5 4 5
## MMP3 0 0 0 0 0 0
## CASP1 3076 2546 2850 2786 2842 5908
## DLAT 145 123 178 224 176 172
## IL18 91 40 106 67 50 77
## CD3E 3121 3228 2939 3225 3226 2589
## MCAM 222 244 271 232 264 199
## WNK1 3150 3684 4016 4525 2934 2684
## TNFRSF1A 2093 2861 3914 5234 4476 3606
## GAPDH 17375 17952 20679 14568 16738 16839
## CD4 4736 3390 3849 3655 2532 3313
## SLC2A3 6606 15235 10424 7398 8799 6683
## CLEC4D 146 416 858 456 329 461
## KLRB1 496 717 786 491 968 309
## CD69 5064 4649 910 288 1031 1061
## CLEC2B 1791 1982 2020 1411 2048 3157
## OLR1 4 46 25 24 42 6
## ABCD2 228 208 160 330 190 136
## LRRK2 5402 6651 7262 11301 4853 10323
## VDR 319 368 478 498 389 293
## TMBIM6 10443 13070 14312 13406 12421 12329
## PFDN5 3970 3256 3217 2448 4854 2877
## SP7 0 0 0 0 0 0
## MUCL1 0 0 0 0 0 0
## CD63 2351 2654 3236 2367 2943 3705
## SUOX 666 857 1187 1162 922 1010
## RPS26 7431 670 713 2478 4527 3024
## RPL41 8626 7639 7096 5305 10403 6340
## IL23A 65 49 27 31 53 30
## DDIT3 583 805 496 287 536 620
## IFNG 36 26 30 37 6 7
## IL22 0 0 0 0 0 0
## LYZ 85835 59545 49952 71646 42042 80945
## CAPS2 6 7 3 5 4 2
## SYT1 0 1 4 0 0 1
## BTG1 12554 11253 9337 7406 6550 7497
## HCAR3 3551 6767 3455 2309 2596 3671
## GJB2 3 2 0 0 0 0
## GJB6 15 26 20 2 17 2
## TNFSF11 3 2 4 4 2 0
## TPT1 60647 55288 52077 38154 71958 44954
## LMO7 82 64 57 85 62 40
## TNFSF13B 2128 2676 2586 1788 2505 5266
## LAMP1 2526 2941 3217 2813 2397 2857
## PSME2 2387 1082 999 1107 1193 3152
## GZMB 749 286 1136 815 614 672
## RPL36AL 2489 2062 2252 1848 2678 1739
## PYGL 2642 8984 6109 6004 4801 7277
## HIF1A 3196 2238 2748 1802 2529 3992
## FOS 71368 64992 54311 16371 10567 5227
## JDP2 559 647 784 686 624 686
## NOXRED1 5 5 13 4 11 12
## SERPINA1 20709 24162 20989 24228 23581 30445
## CDC42BPB 387 268 236 223 140 290
## PLA2G4D 0 0 0 0 0 0
## TRIM69 12 11 23 12 15 31
## SLC51B 0 0 0 0 0 0
## SMAD3 572 603 714 740 807 529
## CYP1A1 0 0 0 1 0 0
## AKAP13 4477 3249 4951 6183 3390 6201
## MEFV 1753 2291 2678 4105 2915 4327
## SOCS1 146 89 51 33 61 130
## ATXN2L 1951 1665 1606 1478 1851 1527
## CD19 134 166 191 97 214 347
## ITGAL 4440 4424 6062 7061 4200 5698
## ITGAM 3592 6238 7251 6264 4400 7103
## ITGAX 3740 5799 5135 4611 7420 6285
## DNAJA2 573 519 621 870 609 640
## SIAH1 127 83 95 212 126 119
## ADCY7 2513 2197 2882 2926 1931 2456
## NOD2 714 489 1247 1031 1017 2140
## CMTM2 1092 2008 3024 2849 2546 1844
## SF3B3 840 933 883 1085 796 768
## PSMD7 574 516 711 706 724 650
## WWOX 48 23 41 43 39 32
## MAF 523 422 694 629 554 381
## SLC7A5 196 216 232 152 277 225
## CXCL16 2232 2163 3028 1033 3421 1706
## XAF1 1878 708 652 659 557 4618
## CD68 4001 2990 3551 3576 2503 4260
## PER1 1544 590 547 189 608 929
## NOS2 1 2 2 0 2 0
## TRAF4 104 118 110 68 89 82
## CCL2 21 14 34 1 4 10
## CCL5 1517 3260 5144 5590 3596 3206
## CCL3 505 620 121 62 144 24
## CCR7 1134 722 484 1066 1316 605
## STAT3 3083 4086 4639 5966 4601 6594
## SOST 0 0 0 0 0 0
## ITGA2B 523 692 296 390 974 346
## EFCAB13 27 22 22 19 16 22
## NPEPPS 672 797 954 1219 932 969
## TBX21 181 149 494 755 330 445
## COL1A1 3 1 0 1 1 2
## MRPS23 98 82 200 233 181 155
## MIR21 7 3 6 5 5 2
## RPS6KB1 312 317 345 460 382 382
## ACE 30 32 21 46 33 46
## ERN1 1116 889 1171 1105 1032 739
## PRTN3 15 8 14 9 18 9
## PLIN5 97 161 147 109 187 115
## RETN 410 210 100 87 49 52
## CCL25 0 1 1 0 4 0
## ICAM1 3518 3516 2042 874 2341 2664
## TYK2 1462 1504 1890 2461 1641 1601
## SMARCA4 646 615 800 848 648 618
## ACP5 213 258 303 228 387 478
## JUNB 36032 31096 42777 18508 35480 16448
## CYP4F22 70 16 14 30 36 61
## JAK3 1945 2024 1877 2041 3259 2702
## JUND 22156 17497 7978 2938 4834 4213
## CEBPA 680 695 828 1221 651 861
## CEBPG 267 164 239 403 231 289
## ACP7 1 0 0 0 1 0
## ZFP36 41583 40258 18163 15631 10266 14721
## TGFB1 4364 5211 4765 5079 5173 5464
## RPS19 12466 10285 9561 7612 13571 8779
## PSG2 0 0 0 0 0 0
## FUT2 1 3 2 3 2 1
## NKG7 2024 2257 4821 4524 3079 3467
## ZNF415 4 2 3 3 15 9
## LILRB2 4437 4372 5012 3812 5536 5507
## LILRA5 2012 3685 2974 3935 6137 3272
## KIR3DL1 21 68 105 89 19 20
## KIR3DL2 43 19 108 60 12 21
## SMOX 159 146 117 97 149 57
## BMP2 5 9 9 3 5 0
## GINS1 9 2 9 7 8 4
## PLCG1 870 724 731 1063 1027 534
## YWHAB 4378 5575 7203 6036 4542 6690
## PI3 1036 1016 1625 750 3044 947
## MMP9 479 2222 3604 4607 1378 1901
## CD40 308 184 184 96 183 204
## PFDN4 49 37 48 45 44 46
## BMP7 0 0 0 0 0 0
## RPS21 5735 4718 4451 3397 6614 3978
## MX1 2401 1283 529 977 463 4615
## PFKL 1159 928 1185 1245 980 1138
## IL17RA 3861 5270 6098 8597 4932 7254
## UBE2L3 719 796 1121 1094 921 1066
## TPST2 832 1310 1374 1408 1303 1072
## XBP1 923 817 1089 1397 1303 936
## UQCR10 495 449 635 527 606 493
## SEC14L2 42 44 18 20 35 23
## APOL6 2697 903 1221 2128 996 4991
## APOL1 1125 512 683 658 569 1641
## TYMP 5191 3844 3548 4231 4013 6892
## BEND2 99 72 73 69 69 23
## PHEX 9 12 14 23 8 0
## TIMP1 1192 1414 2649 1576 2028 1137
## FOXP3 92 67 68 120 77 39
## MSN 17075 23255 25385 24401 19566 24745
## PGK1 7002 8361 9062 6494 8188 8663
## LAMP2 4364 6126 7185 6618 5453 7363
## CD40LG 177 134 163 268 175 61
## IRAK1 1696 1236 1567 1313 1376 1488
## COX2 52863 43316 49415 43591 42967 40652
## GSM3308503 GSM3308504 GSM3308505 GSM3308506 GSM3308507 GSM3308508
## TNFRSF9 153 232 91 135 279 160
## ENO1 6676 7534 7077 6100 6327 7345
## PIK3CD 8297 6481 6150 7949 7804 9212
## PGD 6622 6641 5677 6586 4461 4453
## MTHFR 358 325 296 354 455 497
## TNFRSF1B 16649 13431 13391 12488 12305 13145
## PINK1 794 1053 687 836 837 785
## IFNLR1 43 17 40 27 57 39
## RUNX3 2803 2347 2528 1916 3403 3193
## SH3BGRL3 10008 12800 9026 9492 8824 9180
## CD52 3149 3547 3833 3179 3580 4702
## IFI6 864 1521 4704 1762 623 1167
## ZC3H12A 419 417 283 328 438 388
## UTP11 124 114 90 94 125 215
## JUN 4358 4386 188 1087 1598 303
## KANK4 0 0 0 0 0 0
## EFCAB7 20 20 25 18 36 45
## IL23R 2 1 2 1 1 21
## ADGRL2 0 0 1 0 1 0
## GBP3 276 176 131 208 328 595
## GBP1 953 1418 1274 998 1183 2012
## GBP5 2861 2578 2179 2214 3335 4844
## TGFBR3 614 393 439 259 697 655
## VCAM1 1 0 4 1 6 2
## PTPN22 415 453 333 321 454 611
## CD160 158 52 45 55 85 178
## FCGR1A 1085 1458 1538 752 1348 778
## MCL1 22890 30075 23691 17347 21278 22706
## CTSK 57 80 28 52 68 54
## RORC 46 17 32 14 74 290
## S100A9 170797 166713 179161 154068 107188 102280
## S100A12 7108 5355 6273 4833 3556 4366
## S100A8 69459 68573 74911 68700 40159 39610
## IL6R 4525 4702 5214 5122 4449 6287
## RIT1 1422 1481 1064 1210 1143 1160
## BGLAP 8 8 7 6 11 4
## IFI16 3883 3799 4916 3370 3449 5003
## AIM2 200 141 233 192 210 231
## CRP 0 0 0 0 0 0
## FCGR2A 17439 14330 14482 17933 16627 14082
## HSPA6 2184 2195 1537 1734 1664 2195
## FCGR3A 11434 16009 15859 20344 13783 18872
## SELL 33586 30457 28827 35589 36572 36612
## GLUL 17240 20494 12747 12596 14334 10757
## PTGS2 12879 8593 1852 6688 16253 12228
## CRB1 0 3 0 0 0 2
## KDM5B 390 442 379 405 398 489
## IL10 8 16 7 2 0 4
## YOD1 244 255 237 213 319 261
## HHAT 40 27 18 16 45 36
## TRAF5 338 257 218 249 396 575
## NLRP3 1128 938 815 769 719 813
## LINC01250 0 0 0 1 0 0
## RPS7 6278 8199 7467 5947 7083 9750
## RSAD2 274 521 3346 942 309 753
## FOSL2 3633 3532 2437 3055 3268 3405
## REL 1055 824 749 875 955 1335
## TGFA 810 508 534 558 458 512
## DYSF 5989 5597 7120 7320 5753 4136
## HK2 1557 1155 1005 914 1152 1082
## CD8A 1283 1085 1205 422 1723 1293
## CD8B 537 490 506 157 819 590
## EIF5B 447 463 438 435 541 855
## IL1R1 232 334 203 306 222 222
## RGPD6 70 77 68 87 82 150
## IL1A 0 1 0 0 2 0
## IL1B 1583 980 427 791 3503 2764
## IL37 0 0 0 0 0 0
## IL36RN 0 0 0 0 0 0
## IL1F10 0 0 0 0 0 0
## IL1RN 3275 2409 3311 3738 3015 2418
## NMI 2046 2070 2170 1420 1574 1799
## TNFAIP6 467 348 651 610 493 279
## IFIH1 421 414 637 489 434 705
## SCN1A 0 0 0 0 0 0
## ABCB11 2 0 0 1 0 0
## RBM45 48 54 50 45 81 80
## FRZB 0 0 0 0 0 0
## TFPI 3 4 2 22 5 3
## STAT1 4924 5330 4781 4727 4425 6131
## NABP1 1079 749 723 690 913 779
## SF3B1 4801 5728 3798 4135 4418 5203
## CASP10 313 415 252 337 302 616
## CD28 515 631 423 472 737 1032
## CTLA4 58 101 59 46 55 64
## ICOS 100 154 168 104 211 292
## NDUFS1 614 532 430 498 559 771
## CXCR2 22291 25091 25981 22691 30575 26602
## IRS1 78 50 140 86 49 76
## CCL20 3 2 2 0 1 4
## ATG16L1 262 296 216 226 284 430
## GPR35 85 133 52 75 65 93
## PDCD1 29 15 62 10 36 48
## PPARG 1 4 4 4 1 6
## RPL15 10179 14127 10853 10088 11431 15295
## EOMES 189 59 105 55 232 353
## CX3CR1 2331 1012 1590 1535 1617 3116
## ACKR2 0 0 2 0 0 1
## CCR2 1018 1018 1446 576 987 2901
## CCRL2 54 60 19 59 36 48
## TLR9 80 74 61 74 71 113
## ARHGEF3 1211 899 787 675 1058 1557
## ADAMTS9 0 0 0 1 0 0
## TMEM45A 3 3 0 7 0 5
## CD80 6 4 2 0 3 7
## CD86 833 882 640 545 519 1236
## MIX23 22 28 22 26 31 55
## PLS1 14 14 19 27 21 28
## PTX3 65 62 46 144 21 46
## GOLIM4 101 87 78 64 83 140
## MYNN 328 350 284 292 278 400
## TNFSF10 3759 3652 4172 3934 3764 5525
## ADIPOQ 0 0 0 0 0 0
## SPON2 827 352 245 284 498 436
## S100P 2520 4618 256 3152 3181 2424
## WDR1 6381 6202 5572 6120 5895 6508
## CD38 365 161 61 242 112 338
## PPARGC1A 2 9 3 0 4 8
## TMPRSS11B 0 0 0 0 0 0
## CSN3 0 0 0 0 0 0
## ALB 0 0 2 0 0 0
## CXCL8 64456 44699 4836 30523 16670 12954
## CXCL2 41 59 2 8 1 2
## AREG 19 94 116 6 11 6
## CXCL10 17 15 19 78 16 68
## CXCL13 0 0 4 0 1 0
## SPP1 34 80 11 192 24 79
## HERC6 181 177 366 204 178 245
## NFKB1 1050 1045 1064 890 1336 1503
## SEC24B 472 427 319 403 484 615
## EGF 20 22 8 168 17 13
## IL2 0 2 0 0 1 0
## IL21 2 3 1 0 1 4
## IL21-AS1 1 1 1 1 3 4
## SLC7A11 22 14 11 8 13 14
## IL15 72 76 74 63 65 122
## EDNRA 0 0 0 0 0 0
## TLR2 5139 5358 6952 4612 4803 4470
## FGB 0 0 0 0 1 0
## DDX60 321 294 906 456 341 671
## SPCS3 2082 2126 1680 1665 2339 2773
## TLR3 11 3 5 3 14 24
## OSMR 27 27 22 24 28 33
## GZMK 574 233 459 221 753 845
## GZMA 1162 563 707 426 1157 1338
## ANKRD55 73 144 63 155 64 124
## CENPK 18 108 13 28 20 30
## CAST 2772 2617 2767 2166 2898 2953
## ERAP1 1268 1193 1113 1254 2099 2043
## ERAP2 154 1474 1120 147 1496 2013
## TNFAIP8 1221 1350 1256 1231 1496 2242
## CSF2 2 0 0 0 0 1
## IL5 0 0 0 0 0 0
## IL13 0 0 0 0 1 1
## IL4 6 15 2 2 6 16
## CD14 11945 10171 8801 12641 8644 8509
## CSNK1A1 1626 1872 1482 1714 1766 2635
## PPARGC1B 132 114 81 83 91 157
## TNIP1 5094 4361 5399 5252 4955 4174
## ATOX1 177 199 140 161 128 183
## FAXDC2 120 152 97 368 140 140
## IL12B 0 0 0 2 1 0
## MIR146A 0 1 0 0 0 0
## PDLIM7 2205 2291 1917 1814 1699 1008
## SERPINB1 5456 5821 6545 5004 4673 3922
## SSR1 2267 2386 1927 1953 2181 2893
## CD83 653 293 149 557 267 221
## SOX4 150 171 64 112 57 168
## CMAHP 88 90 68 67 53 130
## HLA-A 45637 39900 46947 41110 40049 41793
## HLA-C 54714 102715 59177 86335 70731 51502
## HLA-B 76295 113315 73201 84654 82750 67320
## MICA 216 138 125 123 120 209
## LTA 49 67 43 68 89 114
## TNF 194 328 71 346 214 216
## HLA-DRB1 6070 2769 2068 2061 2934 4349
## HLA-DQB1 2995 212 279 1625 476 501
## PPARD 277 283 275 275 336 501
## CCND3 3605 5555 5068 3966 3477 3880
## VEGFA 172 205 76 197 75 155
## RUNX2 408 494 373 364 456 549
## IL17A 0 0 0 0 0 0
## IL17F 0 0 0 0 0 0
## PRDM1 462 361 993 306 583 900
## ATG5 381 437 335 311 383 488
## TRAF3IP2 143 168 169 186 143 210
## NCOA7 303 352 364 407 449 609
## SGK1 5419 4803 1717 3373 2360 4748
## IFNGR1 4165 4215 4746 3472 3300 4200
## TNFAIP3 2598 3060 2945 1464 1362 1193
## SOD2 47597 49172 39547 48430 47688 36978
## LPAL2 25 21 10 5 16 29
## PLG 1 1 1 0 0 0
## CCR6 74 41 95 40 90 337
## RAC1 3254 3220 2835 2487 2474 3097
## ZNF316 747 687 671 509 794 554
## AHR 726 1333 1281 465 711 906
## IL6 1 0 2 0 1 2
## TOMM7 1788 1821 1539 1880 1851 2625
## CYCS 620 523 391 353 413 732
## AQP1 4 4 3 7 5 2
## NT5C3A 689 625 640 736 658 640
## EGFR 0 0 0 0 0 0
## CD36 2565 3031 2378 1701 1909 3686
## SAMD9 1975 1890 2688 1890 1919 2285
## SERPINE1 8 11 0 18 5 7
## CUX1 1552 1542 1219 1411 1206 1499
## PSMC2 343 375 336 266 362 605
## NAMPT 70200 53968 53012 51494 46224 35985
## HYAL4 0 0 1 0 0 0
## LEP 14 1 10 13 1 5
## CALD1 5 3 4 89 2 10
## BRAF 651 625 486 694 608 677
## EZH2 67 59 48 46 50 79
## DNAJB6 1628 1535 1184 1477 1482 1641
## CSMD1 1 17 0 0 0 1
## CTSB 6947 5734 4670 4930 4444 8105
## EGR3 962 903 1173 685 1537 414
## TNFRSF10A 129 165 98 169 218 239
## BNIP3L 2533 2866 2039 2303 2326 2445
## DUSP4 21 101 28 14 2 8
## NRG1 111 103 144 29 55 39
## RPL7 7091 9529 7287 7790 8673 11245
## IL7 6 12 14 11 14 22
## GEM 1 1 0 0 1 2
## MYC 542 747 997 661 972 1371
## GPT 2 1 3 0 1 3
## JAK2 1236 1039 877 1083 1171 1413
## CD274 180 165 293 157 340 287
## IL33 0 0 0 0 0 0
## LURAP1L-AS1 0 0 0 0 0 0
## LURAP1L 1 1 1 0 1 0
## TTC39B 87 178 88 148 177 212
## IFNA1 0 0 0 0 0 0
## TEK 8 16 7 14 7 11
## TRBV20OR9-2 0 0 0 0 0 0
## TOMM5 182 240 143 152 197 302
## ANXA1 4931 8379 7412 5343 5648 5509
## ERP44 1478 1265 1038 1073 1215 1352
## ZNF483 18 28 22 22 41 39
## TNFSF15 16 1 3 11 7 9
## TLR4 8853 8700 8067 5289 6517 6853
## PTGS1 498 586 396 1295 440 724
## HSPA5 6432 5821 4627 3533 6900 4262
## FNBP1 3389 3409 3144 3363 3631 4377
## CARD9 189 258 140 107 125 166
## TRAF2 128 116 104 120 159 177
## CLIC3 128 72 78 56 75 80
## IL2RA 45 114 168 81 156 127
## GATA3 207 247 254 229 441 439
## VIM 13506 19826 14222 14235 14010 13498
## CREM 152 191 145 167 125 147
## DKK1 0 0 0 1 0 0
## MBL2 0 0 0 0 0 0
## SAR1A 912 882 688 823 798 1205
## PRF1 3345 1846 1476 1453 2471 3594
## ZMIZ1 1944 1910 1498 1974 1829 2091
## IFIT3 3564 4483 10262 4897 2796 4472
## TALDO1 11621 11012 9108 9013 8819 7495
## IGF2 0 0 0 0 0 0
## INS-IGF2 0 0 0 0 0 0
## IGF2-AS 0 0 0 0 0 0
## INS 0 0 0 0 0 0
## STIM1 1274 1430 1213 1172 1400 1594
## TRIM22 2525 2954 3667 2091 2462 3923
## PTH 0 0 0 0 0 0
## SAA1 0 0 0 0 0 0
## SLC1A2 1 0 0 0 1 2
## FOSL1 33 67 22 31 14 7
## CCND1 13 5 4 5 11 14
## JRKL 82 47 52 78 111 172
## MMP7 0 0 0 1 0 0
## MMP1 2 0 1 8 2 3
## MMP3 0 0 0 0 0 0
## CASP1 3650 3558 3367 2047 2859 3450
## DLAT 199 164 158 145 202 277
## IL18 98 122 88 60 59 125
## CD3E 2345 2660 2450 2590 3752 3920
## MCAM 220 316 198 258 218 247
## WNK1 3678 3471 2964 4040 4002 4298
## TNFRSF1A 4743 4208 4505 4385 5009 5088
## GAPDH 20434 22103 21844 16544 15698 17327
## CD4 3926 3716 2761 4285 3935 5377
## SLC2A3 16273 9685 8282 13073 9638 4980
## CLEC4D 625 612 561 786 379 297
## KLRB1 846 345 466 312 670 1376
## CD69 2195 1731 837 485 482 356
## CLEC2B 2088 1773 1674 1377 1647 1769
## OLR1 10 40 14 288 7 4
## ABCD2 133 138 155 139 297 271
## LRRK2 9174 8987 7176 8839 8122 8193
## VDR 488 353 497 503 443 463
## TMBIM6 14743 15309 11131 12210 12872 14245
## PFDN5 2884 3970 3092 2632 2709 3700
## SP7 0 0 0 0 0 0
## MUCL1 0 0 0 0 0 0
## CD63 3120 4051 2791 3068 2399 2465
## SUOX 1252 1075 859 1164 1009 1205
## RPS26 699 817 639 550 5944 6687
## RPL41 5777 7632 6599 5687 6566 7854
## IL23A 24 39 26 22 39 63
## DDIT3 779 604 325 479 359 304
## IFNG 31 26 1 7 12 5
## IL22 1 0 0 0 0 0
## LYZ 78270 74485 48717 67601 50568 81466
## CAPS2 2 2 2 6 3 9
## SYT1 1 0 8 2 0 4
## BTG1 10093 12139 6425 6992 6979 8575
## HCAR3 4667 3533 3637 3313 5167 3896
## GJB2 0 0 0 0 0 2
## GJB6 13 5 4 33 3 13
## TNFSF11 1 2 6 1 1 0
## TPT1 41646 58783 47547 44091 47413 56172
## LMO7 51 74 45 98 89 120
## TNFSF13B 2507 1670 1966 1994 1997 2028
## LAMP1 3377 3017 2544 2817 2658 2653
## PSME2 1327 1351 958 1064 1038 1512
## GZMB 797 726 565 366 728 959
## RPL36AL 2168 2391 2004 1860 1833 2423
## PYGL 9179 7549 6791 6544 6842 4297
## HIF1A 2045 2325 1843 2285 1874 2020
## FOS 29005 58594 7754 14729 22770 20656
## JDP2 736 1071 1504 656 549 598
## NOXRED1 10 12 5 5 9 6
## SERPINA1 24243 22770 27192 29531 21123 23439
## CDC42BPB 192 206 178 205 197 292
## PLA2G4D 0 0 0 0 0 0
## TRIM69 18 17 23 11 24 12
## SLC51B 0 1 0 0 0 0
## SMAD3 551 465 530 401 674 810
## CYP1A1 2 3 0 2 1 2
## AKAP13 3891 4089 4082 3711 4212 5310
## MEFV 3226 3497 2514 3545 2855 3608
## SOCS1 51 82 124 25 42 38
## ATXN2L 1950 1631 1347 1547 1754 1901
## CD19 171 27 123 60 81 215
## ITGAL 6455 5394 4157 4604 6116 6577
## ITGAM 6213 5901 5748 5887 5140 4601
## ITGAX 7955 6155 5588 5290 5220 5289
## DNAJA2 743 730 636 621 727 984
## SIAH1 115 126 105 127 118 193
## ADCY7 2685 2299 2128 2065 2457 3318
## NOD2 488 1593 806 791 960 1186
## CMTM2 3077 2713 2736 2444 2054 1860
## SF3B3 950 847 751 801 1137 1355
## PSMD7 690 719 588 592 650 816
## WWOX 29 49 22 51 35 57
## MAF 456 452 421 263 582 856
## SLC7A5 195 198 221 230 247 155
## CXCL16 1894 2485 2337 1698 1519 1287
## XAF1 806 782 1744 956 580 1392
## CD68 4102 4443 3489 3254 2399 4813
## PER1 376 892 1712 331 262 347
## NOS2 1 0 0 0 1 0
## TRAF4 76 99 40 53 60 149
## CCL2 29 6 5 11 32 33
## CCL5 3414 2038 2430 2483 3762 3026
## CCL3 617 389 25 220 196 206
## CCR7 587 888 978 1071 1182 2085
## STAT3 5877 5646 5020 5651 5293 5788
## SOST 0 0 0 0 0 0
## ITGA2B 241 270 121 4138 214 312
## EFCAB13 24 20 16 11 15 16
## NPEPPS 1168 1071 847 1038 1019 1299
## TBX21 472 204 214 200 342 463
## COL1A1 0 2 0 1 0 0
## MRPS23 144 167 159 151 175 278
## MIR21 7 9 3 9 5 3
## RPS6KB1 372 330 296 355 387 560
## ACE 15 31 61 18 80 57
## ERN1 1095 1047 1039 805 1359 1201
## PRTN3 0 46 16 89 6 10
## PLIN5 135 163 119 205 144 80
## RETN 35 152 127 247 40 48
## CCL25 0 2 0 0 0 0
## ICAM1 1733 2100 1657 1814 2079 1155
## TYK2 2112 2265 1727 1810 1771 2451
## SMARCA4 677 611 601 610 662 838
## ACP5 213 240 338 229 312 342
## JUNB 37533 39455 10048 23534 27414 9625
## CYP4F22 40 11 11 25 21 36
## JAK3 2447 2055 2226 2075 2489 2102
## JUND 5250 6935 3253 3213 4325 1956
## CEBPA 955 815 714 759 809 908
## CEBPG 310 309 218 211 271 479
## ACP7 1 0 0 0 1 0
## ZFP36 31481 33510 6280 14608 16326 14367
## TGFB1 5394 5221 4750 4649 5307 4210
## RPS19 7135 9601 9149 7376 9436 11233
## PSG2 0 0 0 0 0 0
## FUT2 3 2 1 2 6 8
## NKG7 4006 2398 2285 1858 3725 3405
## ZNF415 6 3 4 10 14 12
## LILRB2 4697 4875 3970 4173 3338 4383
## LILRA5 2850 3762 3151 4193 2580 2512
## KIR3DL1 95 98 8 40 91 76
## KIR3DL2 54 35 41 33 63 54
## SMOX 81 72 59 186 85 69
## BMP2 12 9 7 11 10 4
## GINS1 9 6 5 9 6 15
## PLCG1 653 855 734 687 1127 1482
## YWHAB 5993 6001 5018 5632 5343 6621
## PI3 1306 1272 1799 3039 3401 720
## MMP9 2773 2436 2468 6210 2567 1362
## CD40 165 63 142 147 164 244
## PFDN4 44 42 31 38 45 59
## BMP7 0 0 0 0 0 0
## RPS21 3029 4703 4229 3666 4405 5119
## MX1 1169 1674 3607 2001 556 2352
## PFKL 1215 1176 1022 923 1073 1406
## IL17RA 6312 6120 6473 6948 5746 7043
## UBE2L3 1030 1099 947 1063 1004 1298
## TPST2 1595 1230 1304 1050 1272 1147
## XBP1 1193 1072 976 652 1142 1618
## UQCR10 513 630 563 472 454 616
## SEC14L2 25 45 18 36 27 38
## APOL6 1501 1662 1787 1307 1785 2929
## APOL1 681 647 638 1204 740 762
## TYMP 3633 4322 5462 3419 2641 2308
## BEND2 26 35 22 26 31 18
## PHEX 3 14 3 2 6 20
## TIMP1 1976 1367 1984 1730 1340 1165
## FOXP3 44 69 60 75 78 88
## MSN 26737 25942 19898 22455 21701 21316
## PGK1 8779 9626 8053 7253 7134 7506
## LAMP2 7639 7141 6019 7065 5955 5740
## CD40LG 133 138 162 152 266 378
## IRAK1 1461 1676 1189 976 1123 1438
## COX2 46111 36569 39269 38861 43491 37933
## GSM3308509 GSM3308510 GSM3308511 GSM3308512 GSM3308513 GSM3308514
## TNFRSF9 79 50 189 98 96 127
## ENO1 7726 5901 3601 5810 6053 6072
## PIK3CD 4237 4667 12177 7057 5071 5979
## PGD 4941 7177 6102 3736 4579 6765
## MTHFR 347 325 369 460 356 407
## TNFRSF1B 14716 13765 14498 11567 13222 14211
## PINK1 478 703 1192 681 688 1016
## IFNLR1 20 51 48 83 29 56
## RUNX3 3483 2773 1709 3804 3462 4262
## SH3BGRL3 11079 9299 8466 8954 10673 10699
## CD52 4826 2696 2051 6038 4392 4561
## IFI6 1114 2881 577 1177 712 507
## ZC3H12A 765 368 437 382 487 443
## UTP11 80 50 115 167 102 87
## JUN 8126 2322 436 1404 820 9700
## KANK4 0 0 0 0 0 1
## EFCAB7 17 12 28 54 25 27
## IL23R 4 4 3 8 0 3
## ADGRL2 0 0 1 0 0 0
## GBP3 177 152 350 410 145 204
## GBP1 545 1655 1231 1184 487 525
## GBP5 1742 4456 3146 2378 1347 1100
## TGFBR3 640 446 377 941 629 929
## VCAM1 2 12 1 1 0 0
## PTPN22 318 341 402 574 256 438
## CD160 71 23 68 188 94 127
## FCGR1A 504 958 549 417 258 208
## MCL1 20167 39573 39390 21874 15751 17556
## CTSK 93 75 27 52 30 47
## RORC 28 30 79 100 64 60
## S100A9 168707 167363 145851 89157 79820 102411
## S100A12 5365 6602 4211 2221 2409 3652
## S100A8 66068 61366 60930 33972 29644 42066
## IL6R 2757 3270 8768 4031 3277 3603
## RIT1 1345 1653 1823 1220 991 1331
## BGLAP 7 3 5 8 8 5
## IFI16 1511 2451 5020 3304 1623 2066
## AIM2 56 159 289 179 54 75
## CRP 0 0 0 0 0 0
## FCGR2A 8446 8596 26020 12843 8545 8853
## HSPA6 1366 1351 4992 2975 1377 1584
## FCGR3A 10414 17793 25094 15185 14826 14445
## SELL 18691 42106 45915 30100 24555 38389
## GLUL 15075 16800 22191 11400 10539 13182
## PTGS2 2983 1667 19403 12321 1611 4944
## CRB1 1 1 4 2 2 0
## KDM5B 361 470 810 367 301 351
## IL10 19 29 0 1 2 3
## YOD1 321 652 342 206 251 211
## HHAT 24 26 24 45 25 40
## TRAF5 292 232 401 524 257 344
## NLRP3 685 879 433 476 880 504
## LINC01250 0 0 0 0 0 1
## RPS7 9291 6418 4426 11622 8103 7372
## RSAD2 478 1399 274 584 172 145
## FOSL2 3098 4820 5232 2080 3316 2829
## REL 1013 928 1478 1019 747 965
## TGFA 242 345 1310 412 337 539
## DYSF 3175 6202 8381 2999 2877 3896
## HK2 1006 1361 1754 934 528 1042
## CD8A 1432 1316 590 2134 753 3845
## CD8B 537 487 352 1015 361 1623
## EIF5B 375 253 372 733 345 463
## IL1R1 211 624 529 222 151 206
## RGPD6 94 51 101 126 62 54
## IL1A 0 0 1 0 0 0
## IL1B 567 125 2159 1498 179 539
## IL37 0 0 0 0 0 0
## IL36RN 0 0 0 0 0 0
## IL1F10 0 0 0 0 0 0
## IL1RN 2522 1618 2951 2110 1528 1546
## NMI 1174 1656 1763 1675 1044 1330
## TNFAIP6 202 494 664 596 107 487
## IFIH1 258 348 385 506 269 298
## SCN1A 0 0 0 0 0 0
## ABCB11 0 1 1 0 0 1
## RBM45 62 40 53 80 44 48
## FRZB 0 0 0 0 0 0
## TFPI 3 6 9 5 4 8
## STAT1 2313 4948 5435 4236 2688 2862
## NABP1 525 738 1535 652 353 515
## SF3B1 4625 5058 5640 4963 3871 3867
## CASP10 325 315 386 419 301 259
## CD28 795 365 427 817 500 390
## CTLA4 132 93 37 87 90 69
## ICOS 203 68 131 216 152 107
## NDUFS1 405 409 589 657 462 476
## CXCR2 8207 12434 44849 19140 15068 14241
## IRS1 55 25 53 83 67 55
## CCL20 1 2 0 4 2 4
## ATG16L1 313 315 287 389 301 288
## GPR35 159 106 58 78 173 86
## PDCD1 23 46 21 68 24 54
## PPARG 4 2 3 3 3 1
## RPL15 14182 11033 7417 15632 13941 12001
## EOMES 46 39 135 259 33 194
## CX3CR1 336 132 1788 2250 1060 1123
## ACKR2 2 0 2 1 0 1
## CCR2 590 391 1098 939 496 416
## CCRL2 39 27 48 37 41 29
## TLR9 50 38 157 84 46 55
## ARHGEF3 1037 775 798 1227 1027 1040
## ADAMTS9 0 0 0 0 0 0
## TMEM45A 0 9 2 2 2 5
## CD80 9 7 3 7 2 2
## CD86 1049 766 436 799 918 742
## MIX23 24 20 32 46 20 17
## PLS1 12 15 19 31 13 15
## PTX3 92 80 29 29 45 64
## GOLIM4 60 59 78 100 101 78
## MYNN 305 367 346 384 253 308
## TNFSF10 1481 1641 6207 3941 1642 2078
## ADIPOQ 0 0 0 0 0 0
## SPON2 332 322 585 627 1048 593
## S100P 1891 7214 347 1342 1475 1968
## WDR1 4619 4878 6362 5711 5331 6347
## CD38 171 94 304 267 325 335
## PPARGC1A 0 4 10 3 0 3
## TMPRSS11B 0 0 0 0 0 0
## CSN3 0 0 0 0 0 0
## ALB 0 0 0 0 0 0
## CXCL8 47923 11270 18237 29355 8745 32455
## CXCL2 38 12 2 10 3 10
## AREG 96 731 7 6 48 37
## CXCL10 4 8 15 20 4 16
## CXCL13 0 0 0 0 1 0
## SPP1 21 64 93 65 47 63
## HERC6 128 220 173 274 133 157
## NFKB1 1053 708 1245 1053 679 832
## SEC24B 404 451 665 502 368 394
## EGF 18 10 18 33 74 44
## IL2 0 1 0 0 1 1
## IL21 0 1 1 3 1 0
## IL21-AS1 1 0 2 1 1 0
## SLC7A11 18 22 29 18 5 5
## IL15 86 56 55 91 81 69
## EDNRA 0 0 1 0 0 0
## TLR2 3404 6047 9238 3143 2606 2198
## FGB 0 0 0 0 0 0
## DDX60 241 531 368 465 238 230
## SPCS3 1854 1352 2072 2457 1576 1751
## TLR3 4 4 15 27 13 17
## OSMR 27 41 61 20 33 24
## GZMK 400 412 60 583 243 830
## GZMA 818 440 695 1604 919 1535
## ANKRD55 63 105 55 87 79 52
## CENPK 27 65 16 24 75 62
## CAST 2359 1973 2653 3110 3684 2374
## ERAP1 1551 971 1222 1916 1885 1927
## ERAP2 1260 197 1001 1816 1272 1391
## TNFAIP8 1175 943 1426 2100 1068 1139
## CSF2 0 0 1 0 0 1
## IL5 0 0 0 0 0 0
## IL13 2 0 0 0 0 0
## IL4 0 1 4 4 7 8
## CD14 11430 5906 6420 5936 6090 8437
## CSNK1A1 1238 1277 2466 2087 1188 1486
## PPARGC1B 122 96 60 82 155 94
## TNIP1 4628 4481 4501 4796 3690 5290
## ATOX1 169 184 148 192 212 162
## FAXDC2 140 97 156 168 232 167
## IL12B 1 1 1 0 0 0
## MIR146A 0 0 0 0 0 0
## PDLIM7 1533 1926 2388 1599 1472 1624
## SERPINB1 4038 4431 5807 4224 3582 4679
## SSR1 2128 1830 2170 2651 1909 1876
## CD83 472 176 146 361 388 419
## SOX4 255 256 88 113 223 227
## CMAHP 67 58 86 122 85 82
## HLA-A 41885 38892 39335 36074 41148 38862
## HLA-C 78605 83189 79299 48174 72610 70589
## HLA-B 96574 103762 118220 81270 83117 93884
## MICA 101 89 160 170 109 109
## LTA 40 20 47 79 41 64
## TNF 351 70 183 171 233 219
## HLA-DRB1 3765 3727 2893 5133 4026 2670
## HLA-DQB1 3012 893 2141 1393 398 326
## PPARD 291 297 307 393 310 266
## CCND3 3472 7169 4450 3897 4150 4808
## VEGFA 226 201 140 128 223 131
## RUNX2 453 673 672 504 379 585
## IL17A 0 0 0 1 0 0
## IL17F 0 0 0 0 0 0
## PRDM1 455 936 1118 578 397 558
## ATG5 403 334 366 470 403 393
## TRAF3IP2 232 163 166 237 175 139
## NCOA7 319 343 335 555 285 275
## SGK1 4607 1662 6125 3342 1695 2178
## IFNGR1 2355 4080 5766 3163 2462 2678
## TNFAIP3 4854 6970 956 1299 3108 3290
## SOD2 27061 35668 63236 31867 32016 33848
## LPAL2 17 12 20 14 12 21
## PLG 1 0 0 0 0 0
## CCR6 92 105 245 187 62 81
## RAC1 2752 1883 3880 2570 2912 2806
## ZNF316 665 539 586 811 751 721
## AHR 1130 2366 434 776 720 662
## IL6 3 3 3 1 0 4
## TOMM7 2352 1456 961 2508 1564 1971
## CYCS 490 392 320 686 486 541
## AQP1 1 1 2 0 6 1
## NT5C3A 519 630 742 671 611 667
## EGFR 0 0 0 0 0 0
## CD36 3474 1377 1079 2101 2456 1849
## SAMD9 904 1698 2960 2173 971 1202
## SERPINE1 8 3 14 13 17 10
## CUX1 1426 1708 1270 1023 1470 1474
## PSMC2 340 262 309 475 312 354
## NAMPT 47494 79673 70410 35939 31993 39655
## HYAL4 1 0 0 1 0 0
## LEP 1 3 8 3 20 1
## CALD1 7 2 11 18 15 23
## BRAF 471 653 841 637 432 656
## EZH2 52 26 75 71 53 53
## DNAJB6 1352 1339 1894 1491 1488 1458
## CSMD1 6 1 0 3 5 3
## CTSB 6064 5996 3966 6330 7201 5024
## EGR3 384 439 661 1046 213 347
## TNFRSF10A 155 131 121 167 120 106
## BNIP3L 1958 2510 2352 2355 1846 2109
## DUSP4 98 45 23 16 90 40
## NRG1 170 27 119 162 76 94
## RPL7 11315 7226 5219 11698 9414 8413
## IL7 5 7 20 27 7 10
## GEM 0 0 1 1 1 0
## MYC 779 672 580 1004 580 411
## GPT 2 2 2 1 3 5
## JAK2 744 1209 1078 960 680 922
## CD274 119 96 257 234 73 80
## IL33 0 0 0 0 0 0
## LURAP1L-AS1 0 0 0 0 0 0
## LURAP1L 2 1 0 2 9 0
## TTC39B 180 136 161 220 176 155
## IFNA1 0 0 0 0 0 0
## TEK 0 11 22 11 42 3
## TRBV20OR9-2 0 0 0 0 0 0
## TOMM5 185 170 117 285 206 195
## ANXA1 7603 8304 3871 5225 6695 5353
## ERP44 1195 1223 1137 1306 1038 1161
## ZNF483 38 19 31 47 27 25
## TNFSF15 4 2 3 6 3 0
## TLR4 3322 7666 8897 6213 2914 5616
## PTGS1 787 407 756 565 1313 901
## HSPA5 4185 3462 4609 4466 3962 5051
## FNBP1 2889 2978 3828 3889 3229 3486
## CARD9 174 132 116 149 186 172
## TRAF2 96 104 121 165 104 124
## CLIC3 67 53 108 164 233 144
## IL2RA 121 140 102 108 101 102
## GATA3 218 135 202 514 308 311
## VIM 24562 13843 13366 13031 13995 14497
## CREM 222 226 121 147 166 124
## DKK1 0 0 0 0 0 0
## MBL2 0 0 0 0 0 0
## SAR1A 950 948 974 1027 738 677
## PRF1 1607 1322 2966 4290 2849 3265
## ZMIZ1 1705 1691 2917 1782 2304 2016
## IFIT3 2146 5781 3777 3510 1570 1191
## TALDO1 7856 10071 11830 8116 7931 8004
## IGF2 0 0 0 0 1 0
## INS-IGF2 0 0 0 0 1 0
## IGF2-AS 0 0 0 0 0 0
## INS 0 0 0 0 0 0
## STIM1 1118 1056 1489 1340 1228 1327
## TRIM22 1408 4663 3323 2504 1447 1591
## PTH 0 0 0 0 0 0
## SAA1 0 1 0 0 0 0
## SLC1A2 1 2 1 0 1 0
## FOSL1 64 107 8 22 22 10
## CCND1 3 5 6 4 6 7
## JRKL 36 29 121 151 66 68
## MMP7 0 0 0 1 0 0
## MMP1 0 0 2 2 0 2
## MMP3 0 0 0 0 0 0
## CASP1 2228 3115 2739 2707 2273 2123
## DLAT 102 85 133 271 171 197
## IL18 96 113 57 90 86 95
## CD3E 2584 1796 1419 4962 2554 3050
## MCAM 212 240 308 206 189 223
## WNK1 2517 2625 5055 3256 2725 3621
## TNFRSF1A 2159 3109 7155 3754 3083 2699
## GAPDH 23703 21837 11010 16716 17244 15139
## CD4 3921 2116 1678 4326 4431 2985
## SLC2A3 9679 8485 11856 5695 5399 7605
## CLEC4D 299 957 761 262 263 574
## KLRB1 1027 701 478 1071 926 707
## CD69 1738 1449 172 595 999 1450
## CLEC2B 1332 1491 1909 2073 1253 1144
## OLR1 9 21 17 12 3 20
## ABCD2 173 103 143 255 137 118
## LRRK2 3946 8913 18384 6850 4533 5475
## VDR 398 375 803 377 284 356
## TMBIM6 9634 10434 14530 13996 10965 12073
## PFDN5 4056 2987 1882 3913 3262 2969
## SP7 0 0 0 1 0 0
## MUCL1 0 0 0 0 0 0
## CD63 3075 2701 2684 2319 2519 2743
## SUOX 722 803 1438 1127 921 1094
## RPS26 819 2861 1898 890 3324 721
## RPL41 7314 5549 4130 9414 6963 5979
## IL23A 61 31 32 63 33 23
## DDIT3 562 662 726 418 458 596
## IFNG 47 15 4 15 4 90
## IL22 1 0 0 1 1 0
## LYZ 156200 37943 17349 94208 120265 44499
## CAPS2 5 4 4 2 4 6
## SYT1 3 6 1 5 1 1
## BTG1 9008 14371 7941 8594 6635 11648
## HCAR3 1642 1484 5580 2060 854 1380
## GJB2 1 10 0 1 2 0
## GJB6 25 224 8 2 25 8
## TNFSF11 0 3 5 3 1 4
## TPT1 67120 44502 30937 67968 54084 44794
## LMO7 67 48 71 135 49 60
## TNFSF13B 1633 1862 2016 2312 1034 1367
## LAMP1 2478 2328 2633 2749 2460 2699
## PSME2 1269 1278 739 1257 1279 1137
## GZMB 603 396 697 1149 1285 1127
## RPL36AL 2605 1495 1434 1974 1892 2068
## PYGL 3956 6192 8061 3946 2752 5226
## HIF1A 2550 3900 2517 1654 2109 2190
## FOS 70837 52358 32230 16676 5344 70623
## JDP2 801 2795 787 621 717 714
## NOXRED1 9 10 24 11 1 10
## SERPINA1 24644 19582 28948 21861 21873 19919
## CDC42BPB 215 182 149 215 256 221
## PLA2G4D 0 0 0 0 0 0
## TRIM69 17 19 15 21 7 20
## SLC51B 0 0 0 0 0 0
## SMAD3 626 453 448 746 442 619
## CYP1A1 0 1 0 3 1 0
## AKAP13 3524 5837 5241 3614 3322 3132
## MEFV 1681 2265 6314 2436 2920 3208
## SOCS1 59 266 44 35 32 56
## ATXN2L 1360 1254 1269 1907 1594 1890
## CD19 100 131 184 229 0 112
## ITGAL 4216 3983 5196 5339 5457 5933
## ITGAM 4402 6130 5558 3543 4438 4294
## ITGAX 5099 6443 6948 3585 4024 4632
## DNAJA2 632 658 815 822 494 651
## SIAH1 149 141 201 121 104 93
## ADCY7 1621 1584 3008 2620 2948 2296
## NOD2 451 874 446 1109 830 629
## CMTM2 2095 3047 3068 1864 1876 1952
## SF3B3 614 459 594 1078 673 816
## PSMD7 845 688 579 781 679 646
## WWOX 64 44 23 44 41 25
## MAF 382 434 399 590 406 567
## SLC7A5 211 437 208 180 286 188
## CXCL16 1568 4069 1976 1331 1622 1858
## XAF1 643 1284 657 1025 714 475
## CD68 5627 4141 1897 2800 4946 3573
## PER1 1106 7359 249 334 754 601
## NOS2 1 2 0 1 6 0
## TRAF4 93 74 84 136 90 95
## CCL2 4 0 2 26 0 8
## CCL5 2665 2233 1610 5182 3016 6295
## CCL3 249 32 148 112 59 484
## CCR7 902 471 1017 1543 716 392
## STAT3 3184 4986 9352 4570 3403 4000
## SOST 0 0 0 0 0 0
## ITGA2B 271 131 484 417 784 600
## EFCAB13 21 17 25 22 26 20
## NPEPPS 682 883 1637 961 734 867
## TBX21 242 250 346 621 495 544
## COL1A1 1 0 0 0 0 0
## MRPS23 179 91 123 279 164 178
## MIR21 6 12 9 5 3 3
## RPS6KB1 316 343 417 473 306 341
## ACE 22 38 26 87 44 46
## ERN1 878 2212 2260 1350 897 1429
## PRTN3 23 86 9 8 3 79
## PLIN5 68 142 207 101 55 99
## RETN 108 77 43 39 63 103
## CCL25 0 0 0 0 0 3
## ICAM1 1949 1673 1129 1171 1152 1642
## TYK2 1454 1898 3257 1935 1555 1772
## SMARCA4 533 451 456 866 703 715
## ACP5 288 243 169 460 297 210
## JUNB 42799 23043 23742 22345 11329 40255
## CYP4F22 13 37 6 17 65 85
## JAK3 1546 1596 2337 1981 1362 1532
## JUND 7373 6697 3898 4595 4910 7525
## CEBPA 1121 706 720 535 969 801
## CEBPG 292 179 253 373 278 239
## ACP7 0 0 0 0 1 0
## ZFP36 37491 12781 25978 13303 6540 27311
## TGFB1 4664 4757 4024 5250 5585 5874
## RPS19 10203 7618 5065 12331 9760 9625
## PSG2 0 0 0 0 0 0
## FUT2 3 1 2 4 0 0
## NKG7 2682 2366 2014 5480 3850 5989
## ZNF415 0 1 256 14 7 1
## LILRB2 4948 4803 4560 3206 5412 4622
## LILRA5 2843 2136 2795 2209 2759 3542
## KIR3DL1 125 66 53 26 74 42
## KIR3DL2 37 52 27 32 47 71
## SMOX 127 87 101 82 240 116
## BMP2 3 21 3 5 2 12
## GINS1 10 5 11 10 3 8
## PLCG1 721 542 668 1158 710 715
## YWHAB 4713 4120 5303 6646 4899 5751
## PI3 2709 279 1088 901 696 964
## MMP9 3284 5107 2913 1152 1744 3492
## CD40 122 103 144 239 145 125
## PFDN4 48 25 23 62 58 57
## BMP7 0 0 0 0 0 0
## RPS21 4959 3386 2367 6581 4760 4049
## MX1 638 2183 1198 1027 599 593
## PFKL 919 937 763 1214 1374 1116
## IL17RA 4367 5813 9511 4509 4435 4529
## UBE2L3 819 790 909 1168 933 1028
## TPST2 1042 939 1062 1295 1320 1350
## XBP1 991 787 922 1347 1088 867
## UQCR10 495 415 390 633 599 471
## SEC14L2 45 29 13 48 24 23
## APOL6 855 1838 2183 1706 1016 848
## APOL1 362 547 771 535 668 398
## TYMP 3621 4136 3609 2939 2467 3548
## BEND2 24 10 66 44 103 95
## PHEX 6 4 12 13 11 5
## TIMP1 1907 2379 1606 1016 2080 1383
## FOXP3 77 44 58 61 74 84
## MSN 20885 22709 25201 19608 22480 25266
## PGK1 7607 7916 6840 6675 6778 6914
## LAMP2 4684 6222 9673 5619 5474 6117
## CD40LG 133 95 154 380 166 125
## IRAK1 1591 1766 1151 1503 1611 1499
## COX2 60802 29386 15056 46987 59283 54615
## GSM3308515 GSM3308516 GSM3308517 GSM3308518 GSM3308519 GSM3308520
## TNFRSF9 107 93 119 77 78 100
## ENO1 3292 6795 6136 6768 6746 6060
## PIK3CD 4957 7936 6970 7212 4280 6055
## PGD 2487 4480 4433 6070 4640 4228
## MTHFR 234 563 439 396 366 535
## TNFRSF1B 8044 12324 11735 15495 13051 10954
## PINK1 490 758 861 862 775 762
## IFNLR1 47 70 77 68 78 81
## RUNX3 1845 2913 4229 2512 6539 4391
## SH3BGRL3 5374 9044 9207 11429 13967 10463
## CD52 2628 5277 4042 5178 5992 3435
## IFI6 824 4523 851 6691 968 1778
## ZC3H12A 239 354 348 347 1423 239
## UTP11 106 241 157 178 122 157
## JUN 177 669 2578 736 2526 296
## KANK4 0 0 0 1 0 0
## EFCAB7 26 41 41 28 14 41
## IL23R 3 6 13 5 1 9
## ADGRL2 0 0 0 0 0 0
## GBP3 198 549 87 385 89 239
## GBP1 847 2223 809 3423 431 2179
## GBP5 2200 3789 1651 4595 1584 4785
## TGFBR3 427 477 940 468 1021 1056
## VCAM1 1 1 1 0 7 3
## PTPN22 425 573 631 541 375 634
## CD160 40 90 150 175 192 323
## FCGR1A 181 558 325 982 476 776
## MCL1 13948 27084 16716 22072 22346 22782
## CTSK 25 51 67 27 46 19
## RORC 177 144 269 159 35 117
## S100A9 49688 73813 73550 110677 131510 82837
## S100A12 1173 1278 1091 3391 3090 2199
## S100A8 18228 26371 26505 48372 48350 29092
## IL6R 3556 5349 3635 7202 3785 5777
## RIT1 638 1040 1045 1325 1462 1157
## BGLAP 5 7 8 6 6 5
## IFI16 2319 5275 3051 6031 1287 4672
## AIM2 72 198 65 367 45 207
## CRP 0 0 0 0 0 0
## FCGR2A 6875 10967 10442 11716 7309 13387
## HSPA6 1376 2184 1792 3263 736 2065
## FCGR3A 9917 16987 14700 38299 12123 27122
## SELL 14775 32334 23640 39836 25701 27030
## GLUL 6999 11035 11733 14024 13102 9422
## PTGS2 9079 10174 5280 1938 1031 10868
## CRB1 1 0 0 4 0 2
## KDM5B 330 476 430 594 412 502
## IL10 1 2 0 6 1 1
## YOD1 145 207 229 198 288 169
## HHAT 20 41 32 41 45 36
## TRAF5 268 399 556 303 244 382
## NLRP3 444 853 494 824 828 690
## LINC01250 0 0 0 0 0 0
## RPS7 5505 8607 9598 8685 13987 9173
## RSAD2 511 3461 300 8197 228 831
## FOSL2 1948 2621 2704 2415 4237 2594
## REL 644 907 982 1007 1253 1255
## TGFA 372 429 588 565 279 449
## DYSF 1958 3309 2609 4123 2235 3848
## HK2 726 871 836 1151 650 953
## CD8A 1187 1894 3037 1105 2558 2325
## CD8B 539 899 1069 448 1146 1159
## EIF5B 418 775 715 850 408 644
## IL1R1 111 177 210 146 266 149
## RGPD6 74 108 104 109 66 98
## IL1A 0 0 1 0 0 0
## IL1B 2099 2107 1202 1822 384 1331
## IL37 0 0 0 0 0 0
## IL36RN 0 0 0 0 0 0
## IL1F10 0 0 0 0 0 0
## IL1RN 1309 2929 2004 3912 3272 1953
## NMI 938 2101 1362 2217 818 1622
## TNFAIP6 152 280 242 1683 127 1460
## IFIH1 349 1026 398 1220 300 734
## SCN1A 0 0 0 0 0 0
## ABCB11 0 2 0 0 0 0
## RBM45 33 95 69 77 48 65
## FRZB 0 0 0 2 0 0
## TFPI 1 3 6 2 1 4
## STAT1 3077 6681 3009 8620 2154 6375
## NABP1 424 769 573 559 264 472
## SF3B1 2209 4743 4384 3294 4899 3745
## CASP10 322 657 362 557 280 450
## CD28 800 1143 712 980 434 559
## CTLA4 35 76 53 26 88 27
## ICOS 141 286 141 167 194 224
## NDUFS1 355 739 558 756 427 665
## CXCR2 13337 23761 16032 25115 9459 28680
## IRS1 46 98 93 33 66 80
## CCL20 3 0 0 6 8 1
## ATG16L1 242 377 374 281 340 265
## GPR35 76 80 112 109 141 97
## PDCD1 35 75 73 38 43 111
## PPARG 2 3 2 6 7 4
## RPL15 8435 14527 15203 13888 22464 15612
## EOMES 161 232 396 384 166 607
## CX3CR1 1960 3241 2049 4441 546 3590
## ACKR2 2 2 4 2 0 0
## CCR2 1277 2025 1099 2441 427 2427
## CCRL2 37 62 28 108 29 47
## TLR9 93 108 81 120 43 85
## ARHGEF3 1000 1474 1093 1488 872 1249
## ADAMTS9 0 0 0 0 0 0
## TMEM45A 0 2 4 1 0 0
## CD80 0 6 5 10 3 9
## CD86 485 1218 831 1782 1011 930
## MIX23 28 48 43 39 27 29
## PLS1 17 30 28 17 18 16
## PTX3 14 23 21 53 99 30
## GOLIM4 65 141 109 131 87 112
## MYNN 210 329 343 340 461 337
## TNFSF10 2950 6194 2718 6678 1185 4026
## ADIPOQ 0 0 0 0 0 0
## SPON2 323 371 640 570 773 975
## S100P 1235 1969 1598 3444 2689 98
## WDR1 3842 6555 6096 6707 5108 6405
## CD38 86 295 270 321 278 296
## PPARGC1A 12 1 5 0 1 7
## TMPRSS11B 0 0 0 0 0 0
## CSN3 0 0 0 0 0 0
## ALB 0 0 1 0 0 0
## CXCL8 6921 15955 24901 7046 27758 14849
## CXCL2 1 2 5 3 6 2
## AREG 2 5 7 1 306 7
## CXCL10 6 61 22 83 4 60
## CXCL13 0 0 0 0 0 2
## SPP1 8 46 52 31 84 15
## HERC6 153 493 260 569 105 255
## NFKB1 882 1491 1059 1331 766 1288
## SEC24B 356 597 490 636 415 538
## EGF 19 9 17 20 6 5
## IL2 0 1 0 0 0 0
## IL21 0 1 1 0 0 2
## IL21-AS1 0 1 0 0 1 1
## SLC7A11 0 11 3 8 5 38
## IL15 62 121 97 127 50 89
## EDNRA 0 0 0 0 0 0
## TLR2 1897 4062 2746 4602 3412 7861
## FGB 0 0 0 0 0 0
## DDX60 354 1290 455 1563 184 748
## SPCS3 1479 2586 2576 2393 2149 2481
## TLR3 24 19 19 18 15 20
## OSMR 16 20 18 15 28 22
## GZMK 200 454 1224 922 867 934
## GZMA 608 941 1811 1222 1621 2004
## ANKRD55 32 140 91 81 57 52
## CENPK 42 75 143 50 51 119
## CAST 1518 2865 2473 3307 3323 2520
## ERAP1 968 1891 1568 1950 2101 2386
## ERAP2 980 3290 1540 140 128 174
## TNFAIP8 1259 2075 1675 1901 1072 1824
## CSF2 1 0 0 0 7 0
## IL5 0 1 0 0 1 0
## IL13 0 3 0 1 2 0
## IL4 4 11 8 4 2 3
## CD14 4936 6919 6892 7135 8560 6072
## CSNK1A1 1565 2373 1831 2799 1163 2516
## PPARGC1B 48 141 108 92 84 73
## TNIP1 2300 3684 4158 4880 3927 4187
## ATOX1 96 204 178 266 211 166
## FAXDC2 111 156 140 142 107 114
## IL12B 0 3 0 1 0 0
## MIR146A 0 1 0 0 0 0
## PDLIM7 849 1309 1560 1469 1588 994
## SERPINB1 2486 4446 4072 4564 4429 4002
## SSR1 1377 2627 2396 2975 2497 2500
## CD83 111 360 338 191 831 111
## SOX4 71 123 162 195 225 138
## CMAHP 71 82 127 66 62 60
## HLA-A 25133 56281 48577 56711 43361 42062
## HLA-C 41572 54181 70195 82194 83095 61311
## HLA-B 53616 115903 97340 115083 113383 113862
## MICA 95 162 151 180 116 127
## LTA 59 103 76 63 40 60
## TNF 211 270 159 246 417 116
## HLA-DRB1 1755 5061 5554 5847 3853 3315
## HLA-DQB1 482 1050 1420 1897 765 1009
## PPARD 246 402 329 378 317 327
## CCND3 2412 4759 4220 4047 5894 6586
## VEGFA 76 153 119 122 181 110
## RUNX2 480 581 567 513 549 517
## IL17A 1 0 0 1 0 0
## IL17F 0 0 0 0 1 0
## PRDM1 601 983 552 836 780 1198
## ATG5 276 583 457 497 502 482
## TRAF3IP2 146 243 238 206 191 163
## NCOA7 335 660 372 502 341 553
## SGK1 2460 3707 2863 1944 2128 4032
## IFNGR1 2259 3314 3188 4352 1887 4929
## TNFAIP3 769 1276 897 1353 12478 1452
## SOD2 19115 32084 34246 35588 38183 41788
## LPAL2 15 12 20 8 12 5
## PLG 0 0 2 0 0 0
## CCR6 279 268 186 311 104 195
## RAC1 1930 3010 2669 2993 3321 3485
## ZNF316 424 657 851 376 625 451
## AHR 609 1039 780 959 1527 794
## IL6 0 2 3 1 7 2
## TOMM7 1457 2549 1863 2329 2356 1832
## CYCS 396 754 600 636 660 665
## AQP1 1 6 7 0 2 0
## NT5C3A 417 911 637 1240 522 626
## EGFR 0 0 0 0 0 0
## CD36 1211 3342 1722 2659 2182 1996
## SAMD9 1192 3019 1601 2662 862 1811
## SERPINE1 9 7 11 6 4 8
## CUX1 681 1310 1188 1651 1663 1361
## PSMC2 354 644 419 684 350 505
## NAMPT 18755 30781 32113 36838 40776 41614
## HYAL4 0 0 0 0 0 0
## LEP 15 30 4 6 5 13
## CALD1 16 11 8 7 5 8
## BRAF 405 636 689 548 606 627
## EZH2 42 115 53 64 51 65
## DNAJB6 1020 1627 1313 1368 1423 1741
## CSMD1 3 1 0 5 2 28
## CTSB 2983 6937 4154 8836 5991 4636
## EGR3 329 700 406 68 701 231
## TNFRSF10A 142 220 148 125 98 186
## BNIP3L 1234 2323 1932 2354 2277 2232
## DUSP4 16 47 7 14 39 20
## NRG1 48 22 156 136 41 110
## RPL7 6107 10445 11313 10057 14091 11047
## IL7 11 23 16 18 11 15
## GEM 3 3 2 4 1 0
## MYC 620 1359 868 1013 358 915
## GPT 1 4 4 3 2 1
## JAK2 667 1374 910 1173 692 992
## CD274 76 203 142 570 81 289
## IL33 0 0 0 0 0 0
## LURAP1L-AS1 0 0 0 0 0 0
## LURAP1L 0 1 1 0 0 1
## TTC39B 120 241 218 157 146 162
## IFNA1 0 0 0 0 0 0
## TEK 10 5 13 10 7 24
## TRBV20OR9-2 0 0 0 0 0 0
## TOMM5 164 323 266 279 295 243
## ANXA1 3505 9303 6782 7566 12015 5255
## ERP44 648 1415 1126 1458 1305 1223
## ZNF483 29 45 29 41 30 26
## TNFSF15 11 11 4 14 0 9
## TLR4 3669 6579 4853 6759 2948 7668
## PTGS1 430 555 745 458 458 406
## HSPA5 2331 4457 4064 3821 6322 4451
## FNBP1 2506 4078 4199 3497 3387 3983
## CARD9 142 246 174 204 138 146
## TRAF2 117 193 165 182 129 153
## CLIC3 96 148 148 139 209 263
## IL2RA 119 243 96 106 67 105
## GATA3 327 537 443 386 273 356
## VIM 7562 18381 12143 16609 21123 16310
## CREM 85 134 138 158 257 133
## DKK1 0 0 0 0 0 0
## MBL2 0 0 0 0 0 0
## SAR1A 697 966 845 1364 891 965
## PRF1 2413 2859 3311 4030 1780 5294
## ZMIZ1 1288 2264 1885 1868 2620 1967
## IFIT3 2698 12366 2601 17241 1422 5928
## TALDO1 4693 7860 8058 9015 9016 8102
## IGF2 0 0 0 0 0 0
## INS-IGF2 0 0 0 0 0 0
## IGF2-AS 0 0 0 0 0 0
## INS 0 0 0 0 0 0
## STIM1 931 1397 1297 1270 1735 1351
## TRIM22 1907 5349 2262 5976 1292 3522
## PTH 0 0 0 0 0 0
## SAA1 0 0 0 0 0 0
## SLC1A2 0 2 4 0 3 1
## FOSL1 1 7 13 4 51 4
## CCND1 12 10 13 11 5 12
## JRKL 80 118 122 132 49 98
## MMP7 0 1 0 0 0 0
## MMP1 0 0 0 0 0 0
## MMP3 0 0 0 0 0 0
## CASP1 1791 3328 2684 4101 2035 2856
## DLAT 147 238 224 221 146 247
## IL18 58 110 107 105 96 102
## CD3E 2406 4035 3769 3216 3303 3870
## MCAM 179 245 262 397 273 245
## WNK1 2500 3684 3691 3802 2810 4651
## TNFRSF1A 2676 4680 3927 4733 2519 5198
## GAPDH 7681 12937 14733 17408 21586 13980
## CD4 2983 4895 3363 5895 3576 3308
## SLC2A3 3340 4428 5999 6947 6182 3933
## CLEC4D 232 285 240 540 251 295
## KLRB1 698 643 1815 1407 1657 1577
## CD69 206 425 630 180 2067 425
## CLEC2B 856 1717 1610 2101 1348 1461
## OLR1 12 12 4 19 89 10
## ABCD2 182 263 192 191 136 224
## LRRK2 4732 6946 5279 7629 5153 9184
## VDR 265 493 382 639 268 322
## TMBIM6 7780 14055 13236 14080 12692 14091
## PFDN5 1997 3518 3554 3545 5881 3622
## SP7 0 0 0 0 0 0
## MUCL1 0 0 1 0 0 0
## CD63 1392 2325 2777 2977 4675 2655
## SUOX 683 1162 1192 1285 921 1165
## RPS26 4182 3865 4102 3828 1281 788
## RPL41 4599 7983 8110 8068 11463 8250
## IL23A 44 65 30 70 27 32
## DDIT3 167 270 430 303 417 217
## IFNG 6 14 14 16 33 11
## IL22 0 0 0 0 0 0
## LYZ 58532 49037 36533 130117 83424 113114
## CAPS2 1 6 9 5 9 7
## SYT1 0 9 9 1 2 1
## BTG1 4843 7884 9023 9576 11369 9274
## HCAR3 1672 2070 2340 2464 1611 3100
## GJB2 2 0 2 0 2 0
## GJB6 3 7 10 5 16 1
## TNFSF11 4 5 3 1 17 9
## TPT1 33750 55354 53617 48754 73724 55682
## LMO7 77 110 110 82 47 94
## TNFSF13B 1135 2895 1803 3323 1667 2160
## LAMP1 1534 2726 2349 3034 2588 2378
## PSME2 757 1830 1262 1958 1381 1389
## GZMB 977 959 1134 1278 2132 1634
## RPL36AL 1184 2527 1746 2403 2810 2468
## PYGL 2395 3586 4245 3584 3023 3737
## HIF1A 1235 1829 1830 2999 3127 1701
## FOS 16149 36253 16014 40012 7301 15293
## JDP2 358 697 588 624 874 719
## NOXRED1 3 11 11 3 7 2
## SERPINA1 9683 18343 16343 24123 16675 19963
## CDC42BPB 115 306 221 191 236 202
## PLA2G4D 0 0 0 0 0 0
## TRIM69 7 37 10 17 15 17
## SLC51B 0 0 0 0 0 0
## SMAD3 510 721 814 791 741 678
## CYP1A1 1 1 0 0 2 1
## AKAP13 2789 4818 4074 5276 4556 5974
## MEFV 1933 2717 2886 2858 1825 3292
## SOCS1 27 65 35 99 66 53
## ATXN2L 1052 2032 1949 1270 1562 1438
## CD19 95 132 309 193 128 109
## ITGAL 3513 5031 5193 4801 5364 5473
## ITGAM 1844 3887 3752 4710 5173 4697
## ITGAX 1565 2563 4965 2960 4297 2786
## DNAJA2 528 886 742 913 513 878
## SIAH1 146 240 150 236 158 188
## ADCY7 1484 2981 2555 2085 2717 2438
## NOD2 296 911 629 1152 671 1358
## CMTM2 1044 1575 1952 2913 2173 2453
## SF3B3 712 1166 1058 1180 626 1181
## PSMD7 466 855 747 793 801 731
## WWOX 27 54 52 40 51 36
## MAF 476 753 556 461 445 442
## SLC7A5 149 223 254 210 402 237
## CXCL16 548 1348 1344 1731 1656 1685
## XAF1 599 2769 805 2161 422 817
## CD68 2015 4481 2971 6303 5223 3942
## PER1 130 325 276 202 1973 493
## NOS2 1 1 3 1 5 0
## TRAF4 75 116 131 111 175 100
## CCL2 27 226 40 83 10 21
## CCL5 2412 2802 5426 2888 6637 7174
## CCL3 98 310 153 177 249 310
## CCR7 1089 2188 899 1808 564 1783
## STAT3 3299 5241 4489 5980 2916 5656
## SOST 0 0 0 2 0 0
## ITGA2B 186 248 238 124 127 113
## EFCAB13 18 20 22 21 15 8
## NPEPPS 660 1144 993 850 602 1043
## TBX21 423 411 540 437 483 714
## COL1A1 0 0 0 0 1 0
## MRPS23 171 243 221 276 204 285
## MIR21 4 4 8 3 4 3
## RPS6KB1 298 461 433 349 341 460
## ACE 45 67 49 36 30 31
## ERN1 715 1244 1693 1326 1309 1333
## PRTN3 2 3 23 7 69 4
## PLIN5 38 99 100 61 49 53
## RETN 25 77 32 96 235 334
## CCL25 0 0 0 0 2 0
## ICAM1 427 671 948 1150 2423 820
## TYK2 1251 2350 2340 1867 1147 1641
## SMARCA4 453 870 832 713 657 707
## ACP5 240 457 334 576 327 335
## JUNB 10577 22859 21500 17193 16066 10429
## CYP4F22 13 24 41 36 26 20
## JAK3 1125 1768 1904 1213 970 1081
## JUND 1919 4486 4129 2948 7141 2543
## CEBPA 503 1048 637 1336 1021 636
## CEBPG 295 499 315 503 283 406
## ACP7 1 0 3 0 0 0
## ZFP36 11116 22499 10034 16005 13682 11789
## TGFB1 3038 5072 4842 5107 5168 4308
## RPS19 6440 10671 11139 10281 13830 10252
## PSG2 0 0 0 0 0 0
## FUT2 2 3 2 2 4 3
## NKG7 2359 2984 6015 3381 8003 6837
## ZNF415 5 15 14 10 3 18
## LILRB2 1978 4069 3526 4842 4594 2468
## LILRA5 1338 1576 2214 3931 1550 2127
## KIR3DL1 85 47 107 15 359 35
## KIR3DL2 58 63 73 30 96 33
## SMOX 48 75 94 53 59 35
## BMP2 3 1 3 1 6 11
## GINS1 7 12 7 18 7 7
## PLCG1 737 1373 1164 668 499 911
## YWHAB 3670 6297 5411 6621 4998 5735
## PI3 544 955 608 1419 2372 811
## MMP9 739 1044 909 2691 1499 747
## CD40 107 169 233 234 189 160
## PFDN4 30 58 54 53 65 38
## BMP7 0 0 0 0 0 0
## RPS21 3064 5154 5510 4765 7299 5306
## MX1 1109 4633 939 7442 659 2237
## PFKL 790 1706 1129 1124 927 1229
## IL17RA 3338 5915 4150 6080 3159 6565
## UBE2L3 726 1330 1177 1481 1051 1312
## TPST2 665 1255 1254 840 1395 1348
## XBP1 1110 1759 1186 1626 1459 1699
## UQCR10 396 604 653 755 719 634
## SEC14L2 7 21 20 10 28 16
## APOL6 1375 2529 1309 3651 1056 2901
## APOL1 320 1001 748 1150 422 619
## TYMP 2498 6194 2224 2984 2636 3008
## BEND2 24 21 24 25 11 18
## PHEX 4 22 2 10 13 13
## TIMP1 723 1755 1239 2384 2754 1282
## FOXP3 78 144 59 87 40 67
## MSN 11949 20201 20114 22288 23987 24252
## PGK1 3813 6641 6215 6752 9258 6404
## LAMP2 3455 5559 5232 6886 6083 6493
## CD40LG 198 366 230 317 68 219
## IRAK1 814 1429 1590 982 2119 1189
## COX2 25819 60059 59276 44790 78004 54196
## GSM3308521 GSM3308522 GSM3308523 GSM3308524 GSM3308525 GSM3308526
## TNFRSF9 156 146 134 168 106 121
## ENO1 6184 5960 7203 6737 6283 7027
## PIK3CD 6631 9047 4959 7145 5438 5688
## PGD 4884 5249 5133 4048 4326 4333
## MTHFR 397 383 411 478 440 505
## TNFRSF1B 18163 13045 11307 11246 14472 13965
## PINK1 784 938 725 778 822 715
## IFNLR1 43 70 49 88 93 66
## RUNX3 3492 2074 2087 5164 6669 5541
## SH3BGRL3 11438 8090 10297 9539 12040 10273
## CD52 3331 3970 5650 5752 6243 5275
## IFI6 2059 815 3127 607 2135 504
## ZC3H12A 471 355 907 500 748 597
## UTP11 107 163 86 154 74 87
## JUN 3811 984 14634 2095 8972 6964
## KANK4 0 0 0 0 0 1
## EFCAB7 24 35 14 31 24 18
## IL23R 4 5 0 3 0 4
## ADGRL2 0 0 0 0 0 0
## GBP3 136 205 302 370 192 66
## GBP1 1072 949 1337 1175 1511 495
## GBP5 3427 2101 3445 3374 6763 1452
## TGFBR3 679 470 220 1502 1972 1710
## VCAM1 2 0 0 9 1 17
## PTPN22 326 514 183 639 393 399
## CD160 87 81 105 289 176 195
## FCGR1A 755 385 1855 468 1191 610
## MCL1 19949 26431 14377 23528 19484 22229
## CTSK 59 25 48 41 72 45
## RORC 67 148 38 86 25 26
## S100A9 96845 118387 149710 103311 92239 100421
## S100A12 1877 3247 5526 3049 2181 3144
## S100A8 34686 49499 63535 39866 32019 36797
## IL6R 4835 7530 2463 4974 3390 4136
## RIT1 1262 1539 690 1297 1341 1255
## BGLAP 7 7 12 12 8 4
## IFI16 2854 4585 1452 3658 2107 1850
## AIM2 119 190 148 154 153 84
## CRP 0 0 0 0 0 0
## FCGR2A 13317 18053 9643 12400 9875 10674
## HSPA6 1695 2670 1227 1875 1826 907
## FCGR3A 19521 22188 16305 16406 17265 14070
## SELL 37147 32804 35832 29897 31810 25486
## GLUL 17565 14215 8593 10779 14169 15823
## PTGS2 3976 20120 13124 18859 3719 5872
## CRB1 1 1 0 1 2 1
## KDM5B 395 618 285 412 412 406
## IL10 3 1 3 3 1 6
## YOD1 200 210 66 152 295 334
## HHAT 37 48 27 46 42 54
## TRAF5 291 372 175 569 295 315
## NLRP3 632 677 838 576 626 647
## LINC01250 0 0 0 0 0 0
## RPS7 8433 8679 10362 11562 10368 9774
## RSAD2 942 418 813 289 951 116
## FOSL2 3624 3925 2132 2632 4729 5178
## REL 1219 1486 441 1199 1014 1270
## TGFA 439 944 423 500 329 309
## DYSF 4487 6068 4126 3853 3790 3794
## HK2 1024 1641 1250 1045 750 964
## CD8A 1147 1735 968 4866 4475 2689
## CD8B 624 877 553 1755 1517 1051
## EIF5B 432 650 355 740 517 566
## IL1R1 252 270 124 175 171 221
## RGPD6 72 119 32 122 81 81
## IL1A 1 0 1 0 0 0
## IL1B 267 4850 2608 1195 260 355
## IL37 0 0 0 0 0 0
## IL36RN 0 0 0 0 0 0
## IL1F10 0 0 0 0 0 0
## IL1RN 2744 2969 5471 1705 2706 2623
## NMI 1454 1745 1044 1387 1229 995
## TNFAIP6 647 663 381 642 513 444
## IFIH1 508 559 445 463 485 302
## SCN1A 0 0 0 0 0 0
## ABCB11 0 1 0 0 0 1
## RBM45 46 69 42 73 50 40
## FRZB 0 0 0 2 0 0
## TFPI 5 4 3 5 4 6
## STAT1 4660 3597 3809 3896 5384 2640
## NABP1 511 925 676 715 367 413
## SF3B1 5005 4428 2833 5143 4574 4491
## CASP10 256 476 313 350 226 317
## CD28 451 931 382 741 468 632
## CTLA4 69 38 24 62 85 85
## ICOS 131 247 96 263 134 181
## NDUFS1 491 654 345 690 459 452
## CXCR2 21418 33666 8513 20659 11731 16956
## IRS1 72 86 53 105 63 67
## CCL20 2 3 8 2 1 5
## ATG16L1 227 285 242 425 358 317
## GPR35 91 54 97 99 198 75
## PDCD1 31 75 31 127 21 30
## PPARG 1 2 6 8 2 1
## RPL15 13794 13160 13895 17102 16075 15288
## EOMES 132 206 96 525 266 229
## CX3CR1 839 2057 2047 3375 702 757
## ACKR2 0 4 0 2 0 2
## CCR2 577 2009 1471 1688 375 513
## CCRL2 29 47 41 32 42 40
## TLR9 51 122 31 87 49 37
## ARHGEF3 891 1044 743 1399 1275 1343
## ADAMTS9 0 0 0 0 0 0
## TMEM45A 7 0 0 8 2 1
## CD80 2 6 1 4 3 6
## CD86 965 776 993 839 828 926
## MIX23 17 36 15 43 20 23
## PLS1 15 39 9 29 13 31
## PTX3 49 39 100 47 64 70
## GOLIM4 97 88 81 144 61 96
## MYNN 349 327 191 296 394 334
## TNFSF10 2957 5763 3209 4328 2314 1515
## ADIPOQ 0 0 0 0 0 0
## SPON2 293 152 290 421 597 400
## S100P 3994 3829 1572 2685 3275 3650
## WDR1 6401 6174 5165 6139 6046 5773
## CD38 200 164 150 212 212 178
## PPARGC1A 5 1 7 1 2 1
## TMPRSS11B 0 0 0 0 0 0
## CSN3 0 0 0 0 0 0
## ALB 0 0 0 0 0 0
## CXCL8 22828 26953 86505 65792 28261 66157
## CXCL2 7 4 19 12 5 14
## AREG 13 4 49 4 47 90
## CXCL10 36 13 53 58 30 23
## CXCL13 1 0 0 0 0 1
## SPP1 123 60 20 26 83 54
## HERC6 197 222 151 247 221 159
## NFKB1 888 1534 731 1542 787 894
## SEC24B 420 640 235 540 476 470
## EGF 40 18 41 31 25 29
## IL2 1 0 0 0 1 2
## IL21 1 1 1 3 2 0
## IL21-AS1 0 2 2 1 2 0
## SLC7A11 15 18 10 16 14 8
## IL15 79 51 60 96 95 57
## EDNRA 0 0 0 0 0 0
## TLR2 3334 5959 2211 4765 1931 3506
## FGB 0 0 0 0 0 0
## DDX60 464 469 367 541 487 242
## SPCS3 1865 2509 985 2510 1838 2099
## TLR3 9 25 2 27 12 18
## OSMR 33 31 12 26 29 33
## GZMK 753 678 483 1695 1311 1199
## GZMA 1003 911 687 3109 2413 1822
## ANKRD55 40 99 60 55 23 49
## CENPK 53 22 4 98 31 88
## CAST 2676 2729 2056 2888 2523 2733
## ERAP1 1229 984 1132 1847 1325 1381
## ERAP2 1619 1562 1142 194 2076 1850
## TNFAIP8 1195 1990 668 1820 1111 1426
## CSF2 0 0 0 0 1 0
## IL5 0 0 0 0 0 0
## IL13 1 0 0 1 0 1
## IL4 6 3 4 11 4 4
## CD14 6727 6439 10973 6573 6883 7437
## CSNK1A1 1394 2685 1185 2028 1358 1334
## PPARGC1B 137 104 97 106 112 117
## TNIP1 5115 4781 4032 4431 4862 4225
## ATOX1 193 162 219 161 208 177
## FAXDC2 175 99 180 176 147 195
## IL12B 1 1 0 0 0 2
## MIR146A 0 0 1 0 0 0
## PDLIM7 1714 1190 1347 1204 1626 1163
## SERPINB1 4104 4370 4202 3666 4090 3577
## SSR1 2496 2724 1471 2543 2499 2382
## CD83 496 153 896 202 344 440
## SOX4 174 155 109 151 204 222
## CMAHP 62 53 39 85 69 77
## HLA-A 44967 32831 46448 38741 72263 44443
## HLA-C 119436 61921 75242 74110 73825 41517
## HLA-B 118763 91281 96417 91106 143978 89225
## MICA 95 154 150 198 155 116
## LTA 54 79 52 111 35 68
## TNF 293 356 130 260 368 247
## HLA-DRB1 5207 4626 4989 7378 4675 3913
## HLA-DQB1 343 2159 5142 4450 482 3358
## PPARD 303 341 223 357 298 318
## CCND3 3421 3446 4008 5561 3908 4153
## VEGFA 150 160 162 143 241 216
## RUNX2 573 1025 213 421 542 544
## IL17A 1 0 0 1 0 0
## IL17F 0 0 0 0 0 0
## PRDM1 407 994 320 789 620 674
## ATG5 438 405 250 448 508 451
## TRAF3IP2 213 199 128 184 215 167
## NCOA7 351 501 230 637 376 381
## SGK1 2425 4095 1898 1871 1608 2437
## IFNGR1 2959 4849 1391 3300 1867 2459
## TNFAIP3 3107 1288 10865 2064 5692 5693
## SOD2 48988 48946 22401 35873 42821 39584
## LPAL2 13 11 13 17 25 29
## PLG 0 0 0 2 0 1
## CCR6 65 238 54 185 46 91
## RAC1 2810 3278 2060 2743 2848 3102
## ZNF316 702 354 720 741 864 653
## AHR 891 650 438 884 1085 1082
## IL6 3 6 8 3 7 1
## TOMM7 2180 2302 2065 2659 2341 2824
## CYCS 526 593 473 676 632 615
## AQP1 1 2 1 1 6 2
## NT5C3A 854 696 467 604 766 634
## EGFR 1 1 0 0 0 0
## CD36 2024 2490 3065 2854 2112 2581
## SAMD9 1911 2534 1080 1930 1306 1365
## SERPINE1 7 11 11 12 3 13
## CUX1 1897 1322 1136 1287 1646 1649
## PSMC2 325 455 360 542 348 321
## NAMPT 49625 56933 18217 38523 41560 45742
## HYAL4 0 0 0 0 0 0
## LEP 5 8 0 3 0 0
## CALD1 18 5 11 8 7 15
## BRAF 675 777 388 759 618 729
## EZH2 43 38 61 55 39 67
## DNAJB6 1632 1541 1132 1459 1515 1452
## CSMD1 8 10 4 34 3 0
## CTSB 6420 4435 7023 5304 6646 5269
## EGR3 694 489 1449 666 416 638
## TNFRSF10A 124 200 119 216 150 166
## BNIP3L 2264 2521 1633 1898 1757 2157
## DUSP4 41 11 17 34 38 98
## NRG1 89 66 216 92 125 147
## RPL7 9189 9926 9980 10982 10694 11430
## IL7 17 27 12 22 28 10
## GEM 0 2 1 0 2 2
## MYC 520 1003 290 951 270 468
## GPT 0 1 3 2 1 2
## JAK2 1072 1208 770 1021 880 819
## CD274 126 239 290 209 205 83
## IL33 0 0 0 0 0 0
## LURAP1L-AS1 0 0 0 0 0 0
## LURAP1L 3 0 1 1 1 1
## TTC39B 131 217 75 206 130 156
## IFNA1 0 0 0 0 0 0
## TEK 34 19 1 12 14 5
## TRBV20OR9-2 0 1 0 0 0 0
## TOMM5 208 236 244 342 290 251
## ANXA1 6614 5423 6412 6765 6218 8863
## ERP44 1470 1274 1314 1195 1502 1348
## ZNF483 18 22 14 29 41 25
## TNFSF15 0 10 9 10 3 6
## TLR4 3453 7457 3304 4070 3448 3806
## PTGS1 732 402 941 642 588 984
## HSPA5 7028 4853 7233 6769 6397 6543
## FNBP1 3910 3779 2086 4224 3464 3739
## CARD9 192 121 313 143 117 127
## TRAF2 116 164 113 227 127 120
## CLIC3 119 47 70 129 108 134
## IL2RA 105 124 51 121 51 139
## GATA3 406 328 275 504 320 394
## VIM 18605 13383 17476 12696 13319 16088
## CREM 168 120 91 126 255 227
## DKK1 1 0 0 0 0 0
## MBL2 0 0 0 0 0 0
## SAR1A 713 1055 530 1089 865 818
## PRF1 1720 1654 1083 3916 2222 3203
## ZMIZ1 2856 1956 1318 1905 2168 2314
## IFIT3 4734 4040 5828 2287 5388 1329
## TALDO1 9060 8845 8306 6957 8034 7710
## IGF2 0 0 0 0 0 1
## INS-IGF2 0 0 0 0 0 1
## IGF2-AS 0 0 0 0 0 0
## INS 0 0 0 0 0 0
## STIM1 1308 1356 1002 1585 1453 1342
## TRIM22 2754 2635 2685 2462 2597 1306
## PTH 0 0 0 0 0 0
## SAA1 1 0 0 0 0 0
## SLC1A2 2 3 1 1 4 6
## FOSL1 25 2 72 21 34 36
## CCND1 8 11 8 15 6 5
## JRKL 54 145 65 116 58 65
## MMP7 0 0 0 0 0 0
## MMP1 0 0 4 0 0 4
## MMP3 0 0 0 0 0 0
## CASP1 3689 3177 3605 2774 2752 2373
## DLAT 205 221 111 281 176 183
## IL18 111 105 97 46 93 115
## CD3E 2466 3337 2429 4897 4553 3633
## MCAM 280 298 187 297 272 280
## WNK1 4365 5254 2730 4732 3832 4058
## TNFRSF1A 3559 6349 2968 4228 2643 2760
## GAPDH 21523 16390 20558 15488 18591 19511
## CD4 4487 3654 4514 3803 3733 4391
## SLC2A3 9081 10507 5847 8151 8120 9281
## CLEC4D 516 500 480 269 226 240
## KLRB1 883 1113 615 1265 814 1120
## CD69 856 352 1761 844 1492 1809
## CLEC2B 1750 1896 1477 1716 1791 1462
## OLR1 10 12 12 13 10 17
## ABCD2 121 288 62 262 143 168
## LRRK2 7957 11252 3122 6414 7140 5833
## VDR 403 694 338 366 283 292
## TMBIM6 13950 15972 10348 14388 13053 13244
## PFDN5 3326 3057 3898 3964 3894 3592
## SP7 0 0 0 0 0 0
## MUCL1 0 1 0 0 0 0
## CD63 2770 2219 3197 2494 2689 2917
## SUOX 1100 1325 870 1056 1001 1037
## RPS26 693 600 824 4437 4473 6937
## RPL41 6789 7128 10256 9808 9470 8336
## IL23A 20 46 19 54 18 30
## DDIT3 581 276 511 374 447 410
## IFNG 18 5 17 28 55 56
## IL22 0 0 0 0 1 0
## LYZ 86422 104682 122587 73551 90949 122809
## CAPS2 4 3 0 3 6 5
## SYT1 0 5 4 3 5 2
## BTG1 9187 9394 6725 8707 10584 10487
## HCAR3 2065 5354 4028 3227 1928 2578
## GJB2 0 0 1 0 2 4
## GJB6 9 12 8 4 14 27
## TNFSF11 1 5 2 5 1 3
## TPT1 55581 56498 58020 63295 61692 60491
## LMO7 49 136 47 105 42 72
## TNFSF13B 2899 2475 1741 1699 2291 1467
## LAMP1 2639 2565 2354 2772 3011 3085
## PSME2 1563 997 2055 1264 2137 1134
## GZMB 740 576 414 1221 1635 1486
## RPL36AL 2133 1726 1737 2192 2822 2576
## PYGL 4649 5793 3505 4105 3874 3936
## HIF1A 2282 2408 1269 1768 3121 2456
## FOS 27121 40737 77374 30618 36565 44374
## JDP2 931 698 601 489 772 797
## NOXRED1 11 12 3 5 4 3
## SERPINA1 31582 19133 26627 16184 22694 20753
## CDC42BPB 319 194 240 204 209 273
## PLA2G4D 0 0 0 0 0 0
## TRIM69 14 12 21 6 36 15
## SLC51B 0 0 0 0 0 0
## SMAD3 619 662 494 1038 704 758
## CYP1A1 0 0 1 2 0 2
## AKAP13 4603 6344 2605 5497 4739 5644
## MEFV 3411 3531 1524 2271 2692 2235
## SOCS1 47 27 65 46 66 42
## ATXN2L 1861 1263 1590 1993 1918 1884
## CD19 110 149 99 120 93 107
## ITGAL 5744 5326 4740 6674 7173 5799
## ITGAM 4767 4816 4827 5033 5562 6001
## ITGAX 5221 2853 3835 3540 4400 3209
## DNAJA2 566 910 495 901 641 514
## SIAH1 108 213 71 155 134 131
## ADCY7 2639 2357 2007 3048 2735 2557
## NOD2 654 503 799 462 885 706
## CMTM2 2184 2976 2291 1850 1910 1846
## SF3B3 789 1096 817 1314 756 906
## PSMD7 731 721 682 784 737 755
## WWOX 39 36 29 67 56 36
## MAF 372 520 324 636 591 462
## SLC7A5 294 150 114 242 356 347
## CXCL16 3207 1124 1459 873 1834 2262
## XAF1 1119 692 1007 698 1061 503
## CD68 4929 2951 5108 3039 4067 3853
## PER1 565 221 353 279 892 904
## NOS2 1 0 0 4 0 0
## TRAF4 105 142 75 117 103 106
## CCL2 16 24 23 17 5 6
## CCL5 2509 2403 2826 8687 12381 6846
## CCL3 158 310 418 114 138 219
## CCR7 465 2053 407 1089 310 672
## STAT3 4470 6564 2931 4831 4096 3721
## SOST 0 0 0 1 0 0
## ITGA2B 490 71 635 188 401 617
## EFCAB13 17 17 8 21 13 23
## NPEPPS 842 1292 683 1145 676 832
## TBX21 227 230 217 1042 762 499
## COL1A1 0 1 1 0 0 0
## MRPS23 171 216 165 287 146 150
## MIR21 5 4 3 6 5 5
## RPS6KB1 328 518 189 513 324 360
## ACE 56 30 25 66 82 36
## ERN1 1382 1655 547 1560 1469 1576
## PRTN3 5 1 8 5 44 10
## PLIN5 97 66 111 79 56 50
## RETN 58 29 98 55 39 44
## CCL25 0 1 2 0 1 1
## ICAM1 1843 969 2139 1345 2337 1753
## TYK2 1595 1696 1678 1874 1285 1209
## SMARCA4 742 568 645 855 757 707
## ACP5 330 286 282 355 231 255
## JUNB 31759 17829 41520 28498 37225 25345
## CYP4F22 58 12 59 40 49 49
## JAK3 1733 1474 1452 1885 1426 1263
## JUND 7839 2479 19673 3712 9003 6293
## CEBPA 1207 750 1152 765 956 655
## CEBPG 262 360 234 430 296 282
## ACP7 0 1 0 1 1 3
## ZFP36 16136 21924 42111 15068 19852 18410
## TGFB1 5890 3163 5065 4755 6217 3983
## RPS19 9455 9427 11370 12341 11933 11865
## PSG2 0 0 0 0 0 0
## FUT2 0 2 3 5 1 4
## NKG7 2873 2057 2350 7525 9054 5538
## ZNF415 9 19 8 2 3 3
## LILRB2 5319 3181 4799 3012 4629 3982
## LILRA5 3069 2308 3127 1706 3334 1909
## KIR3DL1 85 92 20 202 182 323
## KIR3DL2 41 27 7 95 119 76
## SMOX 112 41 142 121 86 130
## BMP2 1 10 2 7 3 9
## GINS1 7 13 7 14 5 10
## PLCG1 633 1152 608 1483 741 846
## YWHAB 5723 6206 4891 6129 5543 6387
## PI3 1291 955 757 814 788 588
## MMP9 1837 1907 1556 980 2052 2358
## CD40 133 142 281 216 222 150
## PFDN4 45 55 67 50 44 69
## BMP7 0 0 0 0 0 0
## RPS21 4447 4725 5354 6007 5318 5391
## MX1 1257 1686 1865 891 1535 527
## PFKL 1291 884 1087 1144 1066 980
## IL17RA 5962 6954 3719 4386 3982 3960
## UBE2L3 1107 1242 904 1326 1014 999
## TPST2 1094 942 1086 1922 1897 1373
## XBP1 1121 1418 751 2293 1371 1081
## UQCR10 563 563 596 674 600 564
## SEC14L2 19 30 18 25 44 31
## APOL6 1489 1518 1217 1718 2016 1290
## APOL1 727 595 852 469 932 474
## TYMP 4325 1693 7768 2770 3672 2329
## BEND2 56 17 52 43 24 80
## PHEX 14 18 8 20 7 10
## TIMP1 1835 1222 1559 1039 1227 1868
## FOXP3 51 51 54 77 44 85
## MSN 26327 25482 17940 23251 25382 26242
## PGK1 9062 7422 7303 7274 8096 8063
## LAMP2 7862 8136 4031 5389 6194 6784
## CD40LG 172 296 123 297 128 173
## IRAK1 1560 909 1382 1289 1826 1449
## COX2 62714 42372 43760 57294 61903 75922
## GSM3308527 GSM3308528 GSM3308529 GSM3308530 GSM3308531 GSM3308532
## TNFRSF9 91 205 85 133 99 169
## ENO1 5577 5870 7809 6528 5294 4843
## PIK3CD 7422 8557 6347 5774 5518 5516
## PGD 5896 4525 5444 4160 6386 3770
## MTHFR 377 413 413 371 293 463
## TNFRSF1B 13538 13638 14992 15478 14797 12229
## PINK1 1016 810 871 696 848 556
## IFNLR1 56 66 58 89 24 92
## RUNX3 2947 2585 6521 8168 3651 4470
## SH3BGRL3 10970 8198 11427 10505 12441 10730
## CD52 4470 3599 3990 4751 3337 4204
## IFI6 1064 1183 561 582 1286 1121
## ZC3H12A 314 380 452 820 707 1082
## UTP11 81 154 111 81 78 64
## JUN 7541 419 861 9424 1233 31467
## KANK4 1 0 0 0 0 0
## EFCAB7 34 31 30 31 16 20
## IL23R 4 5 4 3 4 9
## ADGRL2 0 0 0 0 0 0
## GBP3 103 280 223 145 101 171
## GBP1 369 1702 699 511 520 378
## GBP5 696 4022 2017 1757 1707 1892
## TGFBR3 543 556 1248 2327 601 945
## VCAM1 0 0 2 6 3 2
## PTPN22 334 503 398 532 231 233
## CD160 53 109 202 101 66 126
## FCGR1A 217 458 415 621 701 378
## MCL1 17168 22302 19167 21743 32488 31672
## CTSK 32 41 32 97 62 63
## RORC 80 74 135 70 49 66
## S100A9 117873 100078 93447 106268 204459 83899
## S100A12 4001 2595 2599 3193 7449 1963
## S100A8 45285 35929 34700 41710 79786 29520
## IL6R 5428 6343 4828 4052 4075 3195
## RIT1 1133 1152 1169 1329 1995 1292
## BGLAP 8 7 10 7 9 9
## IFI16 1724 3974 2064 1562 2206 1156
## AIM2 82 149 89 71 159 37
## CRP 0 0 0 0 0 0
## FCGR2A 10130 15270 10707 9867 12654 8881
## HSPA6 1604 2628 1193 1179 2396 752
## FCGR3A 19069 20086 15848 14669 16127 6061
## SELL 40397 36546 25949 33152 52298 26857
## GLUL 10372 12403 11247 16273 19594 13598
## PTGS2 3839 15573 2183 2804 2372 6995
## CRB1 4 1 1 2 2 0
## KDM5B 437 549 342 478 629 467
## IL10 0 1 3 7 6 3
## YOD1 166 173 244 319 388 277
## HHAT 41 27 45 38 32 47
## TRAF5 318 362 299 333 264 410
## NLRP3 517 692 810 813 885 1075
## LINC01250 0 0 0 0 0 0
## RPS7 9502 7524 9187 10137 9456 10425
## RSAD2 291 730 111 130 348 244
## FOSL2 2775 3403 3357 5826 4789 4363
## REL 770 1188 1033 1222 1232 1251
## TGFA 582 643 407 348 655 383
## DYSF 4991 4869 4081 3463 6745 2419
## HK2 1066 1445 918 688 962 581
## CD8A 1445 1216 1699 3031 1198 2400
## CD8B 1414 803 1000 929 660 1483
## EIF5B 548 680 630 607 381 444
## IL1R1 259 189 188 267 318 249
## RGPD6 80 137 83 103 86 65
## IL1A 0 0 1 0 0 0
## IL1B 144 1533 171 264 259 1105
## IL37 0 0 0 0 0 0
## IL36RN 0 0 0 0 0 0
## IL1F10 0 0 0 0 0 0
## IL1RN 2840 2020 2256 2487 3113 4210
## NMI 1125 1515 1348 1188 1308 674
## TNFAIP6 596 929 375 226 512 506
## IFIH1 215 593 327 295 301 411
## SCN1A 0 0 0 0 0 0
## ABCB11 0 1 1 1 2 1
## RBM45 44 71 57 52 49 33
## FRZB 0 0 0 0 0 0
## TFPI 2 9 10 3 3 7
## STAT1 2304 5607 3112 2544 2865 2442
## NABP1 439 764 279 517 656 762
## SF3B1 4204 4224 4448 4920 5929 4263
## CASP10 262 492 259 242 267 367
## CD28 552 698 504 635 859 773
## CTLA4 52 24 46 87 101 85
## ICOS 173 165 168 171 256 224
## NDUFS1 469 700 455 519 510 374
## CXCR2 17753 31648 18232 14569 20800 13408
## IRS1 117 80 121 76 88 129
## CCL20 0 2 2 1 0 11
## ATG16L1 257 292 280 326 299 372
## GPR35 72 86 155 123 109 100
## PDCD1 39 30 65 48 20 31
## PPARG 1 0 9 10 3 2
## RPL15 15603 11017 15653 14913 14137 16443
## EOMES 62 283 297 245 85 154
## CX3CR1 490 2209 1173 662 233 436
## ACKR2 1 0 4 0 1 0
## CCR2 304 1448 784 443 236 334
## CCRL2 10 51 30 17 41 100
## TLR9 82 93 89 48 52 57
## ARHGEF3 760 1049 1209 1006 953 1413
## ADAMTS9 0 1 0 0 0 0
## TMEM45A 0 1 7 3 0 1
## CD80 4 5 3 3 2 6
## CD86 681 886 967 716 542 611
## MIX23 24 29 26 24 23 27
## PLS1 25 22 26 32 18 18
## PTX3 37 30 53 79 37 71
## GOLIM4 51 131 108 78 57 48
## MYNN 260 345 292 389 425 430
## TNFSF10 2086 4975 2098 1195 2038 1071
## ADIPOQ 0 0 0 0 0 0
## SPON2 291 363 1061 942 192 399
## S100P 4610 3239 1480 1935 2852 198
## WDR1 5656 6224 7402 5476 4882 3963
## CD38 161 259 216 118 243 244
## PPARGC1A 6 13 2 10 4 4
## TMPRSS11B 0 0 0 0 0 0
## CSN3 0 0 0 0 0 0
## ALB 0 0 0 0 0 0
## CXCL8 43100 18887 8873 40866 26869 119038
## CXCL2 3 6 3 6 4 53
## AREG 17 2 19 137 73 131
## CXCL10 15 33 22 5 10 17
## CXCL13 0 0 0 0 1 0
## SPP1 34 94 7 74 48 28
## HERC6 245 216 137 149 147 164
## NFKB1 704 1391 970 923 969 826
## SEC24B 418 645 414 459 525 412
## EGF 27 27 46 32 10 26
## IL2 0 0 0 0 1 0
## IL21 0 0 0 0 0 0
## IL21-AS1 1 0 0 0 1 1
## SLC7A11 12 9 11 15 11 16
## IL15 38 88 61 66 46 36
## EDNRA 0 0 0 0 0 0
## TLR2 3765 3303 3036 3553 6568 2605
## FGB 0 0 0 0 0 1
## DDX60 267 579 222 257 252 238
## SPCS3 1580 2245 2045 2198 1888 1697
## TLR3 3 18 13 14 3 14
## OSMR 30 38 18 42 48 34
## GZMK 562 566 1243 1754 1096 760
## GZMA 704 935 1862 1983 830 1295
## ANKRD55 117 89 61 46 64 56
## CENPK 81 27 64 32 66 138
## CAST 1965 2442 3083 2325 2026 2818
## ERAP1 1080 1439 1801 1912 805 1508
## ERAP2 2503 167 3582 1660 159 1267
## TNFAIP8 1265 1701 1319 1349 1215 1347
## CSF2 0 0 2 0 2 1
## IL5 0 0 0 0 0 0
## IL13 0 2 0 0 0 0
## IL4 5 16 3 3 1 1
## CD14 6375 7170 9599 10374 9527 6414
## CSNK1A1 1299 2465 1410 1428 1420 1153
## PPARGC1B 93 94 97 105 88 123
## TNIP1 4931 4566 4890 4423 5149 4210
## ATOX1 210 141 173 174 159 172
## FAXDC2 147 154 225 161 100 158
## IL12B 1 0 0 2 1 1
## MIR146A 0 1 1 0 1 0
## PDLIM7 2110 1268 1636 1566 2517 1418
## SERPINB1 3136 4122 4082 3934 4661 4245
## SSR1 2189 2398 2377 2466 2048 1897
## CD83 297 180 447 306 488 1508
## SOX4 201 133 218 202 164 265
## CMAHP 55 46 41 80 51 86
## HLA-A 35260 42159 49148 45291 43929 41733
## HLA-C 66626 59213 74700 73508 107757 72130
## HLA-B 84037 87641 95814 129678 108955 76298
## MICA 167 194 85 109 87 77
## LTA 84 61 51 53 53 72
## TNF 200 236 255 312 204 165
## HLA-DRB1 3934 2270 3944 3274 2431 4801
## HLA-DQB1 1088 307 857 2884 337 2778
## PPARD 377 396 362 299 307 301
## CCND3 4555 3497 4870 4953 4834 4010
## VEGFA 213 108 142 186 159 197
## RUNX2 546 547 517 588 747 512
## IL17A 0 0 0 0 0 0
## IL17F 0 0 0 0 0 0
## PRDM1 335 768 710 915 606 465
## ATG5 365 425 393 437 354 309
## TRAF3IP2 271 196 199 187 205 199
## NCOA7 252 463 308 388 405 270
## SGK1 2534 3804 2085 2018 3604 3350
## IFNGR1 2081 4056 2372 2360 2636 1836
## TNFAIP3 2982 1181 3592 9262 6546 18853
## SOD2 29299 44049 38873 39353 56679 39135
## LPAL2 4 16 19 30 5 22
## PLG 0 1 0 1 0 0
## CCR6 93 157 96 75 108 103
## RAC1 2926 2734 3423 2935 3292 2116
## ZNF316 727 540 699 876 757 1048
## AHR 586 633 949 1550 1638 946
## IL6 3 3 0 3 3 21
## TOMM7 2864 1950 2426 2914 2215 2114
## CYCS 531 518 610 650 498 840
## AQP1 1 1 2 6 1 1
## NT5C3A 716 640 634 641 742 595
## EGFR 0 0 0 0 0 0
## CD36 1750 1860 2477 1967 1261 1167
## SAMD9 1342 2253 1177 1284 1340 1141
## SERPINE1 9 11 6 5 7 12
## CUX1 1656 1510 1617 1696 1563 1412
## PSMC2 249 442 350 334 299 259
## NAMPT 41907 37876 32415 51774 82191 37150
## HYAL4 0 0 4 0 0 0
## LEP 4 3 2 1 8 1
## CALD1 4 19 14 15 4 10
## BRAF 716 716 637 736 660 741
## EZH2 46 49 40 80 39 67
## DNAJB6 1412 1732 1691 1582 1727 1179
## CSMD1 0 9 8 1 4 0
## CTSB 5105 5239 9230 5836 4610 3624
## EGR3 428 245 435 795 1121 483
## TNFRSF10A 115 160 95 124 132 159
## BNIP3L 2124 2296 1928 2074 2186 1639
## DUSP4 27 21 41 154 84 71
## NRG1 14 91 103 80 36 94
## RPL7 13198 8001 10976 11015 10025 12733
## IL7 6 18 16 14 14 16
## GEM 0 1 0 1 1 2
## MYC 633 763 766 320 474 312
## GPT 0 0 3 1 0 4
## JAK2 888 1125 861 695 909 809
## CD274 46 245 97 99 96 94
## IL33 0 0 0 0 0 0
## LURAP1L-AS1 0 0 0 0 0 0
## LURAP1L 0 1 3 0 0 1
## TTC39B 164 208 120 142 144 213
## IFNA1 0 0 0 0 0 0
## TEK 1 75 46 13 5 5
## TRBV20OR9-2 0 0 0 0 0 0
## TOMM5 190 229 248 249 198 201
## ANXA1 5928 5457 7900 8946 7030 5408
## ERP44 1241 1274 1419 1217 1340 1157
## ZNF483 35 41 19 37 22 50
## TNFSF15 2 3 1 5 2 1
## TLR4 5628 6796 3895 4245 6307 4323
## PTGS1 776 771 980 648 360 639
## HSPA5 4453 3869 8121 6507 7423 7069
## FNBP1 3801 3780 4443 3730 3247 2669
## CARD9 87 185 143 121 70 149
## TRAF2 123 176 122 142 116 107
## CLIC3 64 104 342 155 59 123
## IL2RA 83 115 94 77 75 87
## GATA3 362 364 509 383 248 353
## VIM 17603 11337 19610 16477 20516 16090
## CREM 125 126 183 296 285 175
## DKK1 0 0 0 0 0 0
## MBL2 0 0 0 0 0 0
## SAR1A 581 955 678 880 1024 773
## PRF1 1032 2944 2685 3268 1252 1344
## ZMIZ1 1741 2364 2817 2433 2449 2823
## IFIT3 2762 4706 1649 1117 2781 2651
## TALDO1 10536 9616 9529 7853 11851 7496
## IGF2 1 1 0 0 0 0
## INS-IGF2 1 1 0 0 0 0
## IGF2-AS 0 0 0 0 0 0
## INS 0 0 0 0 0 0
## STIM1 1333 1292 1608 1404 1172 1284
## TRIM22 1316 2838 1471 1435 1509 1268
## PTH 0 0 0 0 0 0
## SAA1 0 0 0 0 0 0
## SLC1A2 1 0 1 2 8 3
## FOSL1 28 7 22 51 110 69
## CCND1 5 14 7 6 5 8
## JRKL 88 126 68 66 43 66
## MMP7 0 0 0 0 0 0
## MMP1 0 2 2 0 0 0
## MMP3 0 0 0 0 0 0
## CASP1 1912 3394 2397 1853 3069 1562
## DLAT 201 197 243 187 128 138
## IL18 83 96 73 97 90 77
## CD3E 4147 2859 3938 4460 2571 4195
## MCAM 253 219 230 307 215 302
## WNK1 4015 4963 4140 3872 3511 4211
## TNFRSF1A 2956 5062 4123 2924 3793 2899
## GAPDH 18810 14484 21199 20942 21171 14966
## CD4 3666 3783 3771 2505 2692 3516
## SLC2A3 10259 5065 8341 7020 15963 9088
## CLEC4D 322 319 202 337 502 186
## KLRB1 1084 746 1192 1581 1422 1434
## CD69 1299 231 1060 1910 1209 6309
## CLEC2B 1242 1611 1302 1434 2037 1418
## OLR1 7 6 6 88 5 13
## ABCD2 139 253 128 142 161 185
## LRRK2 6652 9527 5947 5202 8587 4311
## VDR 409 633 368 326 517 333
## TMBIM6 13347 14363 14338 12145 13557 11928
## PFDN5 3486 2824 3480 3456 3750 3987
## SP7 0 0 0 0 0 2
## MUCL1 0 1 0 0 0 0
## CD63 2635 2223 2856 3248 3356 2562
## SUOX 1032 1299 1125 1025 917 772
## RPS26 4269 5067 4171 877 6495 763
## RPL41 8601 6561 8850 8649 7871 9740
## IL23A 40 47 24 34 46 51
## DDIT3 424 229 422 443 826 725
## IFNG 12 8 9 42 16 74
## IL22 0 0 0 0 0 1
## LYZ 101968 37839 66522 78408 48341 71176
## CAPS2 6 8 6 5 3 4
## SYT1 2 3 0 8 6 3
## BTG1 9648 8330 8181 10595 10126 14324
## HCAR3 2406 2520 2062 1654 2795 4374
## GJB2 0 0 1 0 0 2
## GJB6 14 2 6 11 37 9
## TNFSF11 0 7 1 1 3 2
## TPT1 65216 26276 59038 57818 57005 67118
## LMO7 87 88 72 46 74 65
## TNFSF13B 1230 2260 1613 1777 1899 2208
## LAMP1 3056 2704 3197 3038 2971 2541
## PSME2 908 1283 1308 1080 1031 1003
## GZMB 434 926 1358 1793 420 1153
## RPL36AL 2704 2103 2287 2667 2272 2026
## PYGL 5636 4580 4729 3708 7481 3083
## HIF1A 1310 2283 1741 2590 4343 3173
## FOS 57739 20194 4170 33439 13675 82548
## JDP2 885 583 759 807 1115 662
## NOXRED1 10 6 4 8 6 11
## SERPINA1 18805 17291 21779 22363 23192 26026
## CDC42BPB 142 283 232 224 170 229
## PLA2G4D 0 0 0 0 0 0
## TRIM69 6 18 19 18 10 7
## SLC51B 0 0 0 0 0 0
## SMAD3 534 613 720 843 552 651
## CYP1A1 0 0 0 1 0 1
## AKAP13 3774 5321 4304 4936 5082 3819
## MEFV 2316 4064 3294 2432 2522 1772
## SOCS1 53 25 49 55 36 141
## ATXN2L 1933 1541 2131 1935 1385 1995
## CD19 76 138 126 99 102 184
## ITGAL 4134 4985 6016 6710 4620 4805
## ITGAM 5717 4725 6015 5687 6702 4091
## ITGAX 3461 3419 3678 5294 7566 5273
## DNAJA2 537 844 606 531 716 652
## SIAH1 86 198 101 128 160 128
## ADCY7 2515 2662 3402 2704 1992 2299
## NOD2 276 566 673 361 1003 864
## CMTM2 2591 2542 1700 1962 4285 1977
## SF3B3 761 1094 1080 789 564 911
## PSMD7 655 743 681 696 829 596
## WWOX 45 39 65 49 62 48
## MAF 328 388 427 606 271 483
## SLC7A5 190 137 405 294 412 260
## CXCL16 1547 1317 1690 1959 2878 2198
## XAF1 584 899 644 535 582 538
## CD68 3225 3415 4959 3302 3317 2505
## PER1 482 241 597 1270 1696 1349
## NOS2 3 0 0 1 0 5
## TRAF4 82 93 112 125 102 168
## CCL2 8 19 7 11 12 6
## CCL5 2363 2583 5819 9185 2758 5437
## CCL3 60 211 35 72 33 740
## CCR7 1175 1522 629 386 743 871
## STAT3 3922 6267 4476 3887 4494 2974
## SOST 0 0 0 0 0 0
## ITGA2B 273 365 824 302 181 260
## EFCAB13 32 25 26 18 22 27
## NPEPPS 756 1108 821 724 900 747
## TBX21 172 360 509 774 201 476
## COL1A1 1 1 0 0 0 2
## MRPS23 138 210 189 167 147 87
## MIR21 6 5 7 13 5 7
## RPS6KB1 354 462 377 379 374 314
## ACE 38 42 67 77 93 46
## ERN1 1087 1485 1324 2222 1519 1398
## PRTN3 6 4 11 31 3 10
## PLIN5 85 96 79 80 98 104
## RETN 54 40 90 188 61 56
## CCL25 0 1 3 1 0 0
## ICAM1 1061 1150 1489 1494 2460 2943
## TYK2 1497 1874 1526 1563 1188 1348
## SMARCA4 787 726 841 815 594 719
## ACP5 209 272 467 222 180 280
## JUNB 33970 15952 12555 32964 35821 32053
## CYP4F22 11 52 34 18 16 22
## JAK3 978 1716 998 1645 1830 1962
## JUND 10655 2390 6677 7916 6604 25113
## CEBPA 913 690 1071 1041 1010 494
## CEBPG 214 335 322 284 269 239
## ACP7 1 0 1 1 1 0
## ZFP36 16542 14747 8075 17819 13352 32898
## TGFB1 5736 3501 8274 5578 5869 4838
## RPS19 11102 8579 12304 11587 10389 12171
## PSG2 0 0 0 0 0 0
## FUT2 5 2 2 1 4 5
## NKG7 2190 2728 5354 8312 2213 5967
## ZNF415 9 12 7 8 3 22
## LILRB2 4003 3592 4388 3796 4945 4082
## LILRA5 2575 2099 2871 2018 3685 1997
## KIR3DL1 31 28 264 217 37 82
## KIR3DL2 23 68 59 79 17 45
## SMOX 112 93 157 106 65 150
## BMP2 3 9 0 4 10 3
## GINS1 6 12 3 9 10 2
## PLCG1 909 899 819 851 708 880
## YWHAB 5560 6621 6698 6181 5528 4819
## PI3 348 1025 880 717 1146 620
## MMP9 3888 1931 1995 2148 5709 566
## CD40 98 126 181 88 101 101
## PFDN4 44 52 45 67 72 64
## BMP7 0 0 0 0 0 0
## RPS21 6370 4013 5684 5649 5242 6143
## MX1 1281 2255 516 415 1024 1059
## PFKL 1025 1252 1427 1051 842 935
## IL17RA 5985 6817 5698 4345 5519 3274
## UBE2L3 1035 1110 1237 953 981 732
## TPST2 1237 913 1746 1708 1144 1227
## XBP1 823 1381 1664 1202 1230 902
## UQCR10 529 540 668 569 543 420
## SEC14L2 82 13 35 45 36 62
## APOL6 641 2440 1075 1233 1123 991
## APOL1 362 1080 729 476 475 480
## TYMP 2951 3907 4192 2905 2887 2320
## BEND2 65 41 79 33 20 43
## PHEX 13 13 23 6 2 22
## TIMP1 996 1933 1879 1857 2783 1218
## FOXP3 78 71 55 68 43 62
## MSN 25884 23598 29667 25346 28530 21476
## PGK1 7117 7060 7848 8427 9359 6684
## LAMP2 7881 7143 6309 6240 8092 5330
## CD40LG 226 268 178 159 134 118
## IRAK1 1549 1090 1841 1893 1518 1485
## COX2 62176 48013 67885 58774 44794 57900
## GSM3308534 GSM3308535 GSM3308536 GSM3308537 GSM3308538 GSM3308539
## TNFRSF9 142 133 77 97 184 166
## ENO1 5491 6502 6299 6624 6847 8162
## PIK3CD 7220 6685 7445 6432 5920 6378
## PGD 4300 4487 5968 5086 4672 5467
## MTHFR 584 413 360 388 474 406
## TNFRSF1B 12408 10891 16164 12847 12347 12645
## PINK1 681 642 783 709 682 787
## IFNLR1 57 42 62 50 79 48
## RUNX3 4066 3307 2798 3517 4758 2429
## SH3BGRL3 9405 8684 11228 10738 11069 10639
## CD52 5375 3953 3752 5399 5953 3765
## IFI6 1011 892 3096 593 1020 511
## ZC3H12A 505 447 508 675 421 701
## UTP11 82 118 111 101 121 134
## JUN 21511 8569 4494 7318 8452 11637
## KANK4 1 0 0 1 0 0
## EFCAB7 42 38 28 17 35 24
## IL23R 10 0 4 2 11 3
## ADGRL2 0 0 1 0 1 0
## GBP3 276 315 190 219 228 144
## GBP1 719 1709 1413 553 713 674
## GBP5 1909 4611 3145 2664 2863 1254
## TGFBR3 544 685 549 521 939 309
## VCAM1 2 4 2 0 3 1
## PTPN22 388 464 438 351 520 303
## CD160 214 222 32 74 275 136
## FCGR1A 406 996 585 522 432 721
## MCL1 23689 23615 24264 21820 17344 22244
## CTSK 81 45 59 58 50 71
## RORC 77 35 61 55 72 47
## S100A9 99827 95727 116372 113883 92054 136886
## S100A12 3449 2773 2487 3177 2287 3595
## S100A8 39625 38390 42997 42504 33315 55654
## IL6R 4106 4348 4793 3894 3612 2546
## RIT1 1062 937 1458 1667 1035 1491
## BGLAP 9 8 10 5 7 13
## IFI16 2180 3045 3897 1749 2606 2492
## AIM2 153 108 125 74 137 119
## CRP 0 0 0 0 0 0
## FCGR2A 11754 11015 14864 10970 8629 15900
## HSPA6 1614 1848 2389 1388 2290 1853
## FCGR3A 14421 10612 21185 14348 17373 15192
## SELL 32955 36599 40746 27746 25838 33086
## GLUL 12042 12619 26321 20318 13072 18752
## PTGS2 14331 28297 6435 4718 4561 29543
## CRB1 0 1 0 0 0 0
## KDM5B 426 392 620 441 360 448
## IL10 7 1 5 4 4 3
## YOD1 219 208 226 343 231 192
## HHAT 33 40 29 26 45 34
## TRAF5 458 380 309 343 533 369
## NLRP3 777 472 773 916 515 1403
## LINC01250 1 0 0 0 1 0
## RPS7 8845 8137 7902 11638 12392 8312
## RSAD2 387 375 2582 119 337 147
## FOSL2 3234 2888 4248 5509 2590 2376
## REL 1005 943 1053 1143 931 862
## TGFA 482 575 831 627 388 515
## DYSF 4199 4272 4265 3427 2732 4741
## HK2 961 1441 1263 916 802 969
## CD8A 1121 2271 1179 989 2729 395
## CD8B 762 1023 648 641 1421 458
## EIF5B 495 586 637 387 584 422
## IL1R1 201 223 250 289 191 272
## RGPD6 57 73 66 76 79 47
## IL1A 1 2 0 0 0 1
## IL1B 1365 2055 659 420 375 5000
## IL37 0 0 0 0 0 0
## IL36RN 0 0 0 0 0 0
## IL1F10 0 0 0 0 0 0
## IL1RN 2540 2319 4508 2516 1431 4998
## NMI 1356 1580 2227 1569 1238 1589
## TNFAIP6 522 714 541 242 274 336
## IFIH1 376 494 607 233 364 299
## SCN1A 0 0 0 0 0 0
## ABCB11 0 0 0 0 2 3
## RBM45 57 61 68 55 82 47
## FRZB 0 0 0 0 0 0
## TFPI 2 1 3 2 2 2
## STAT1 3140 6044 6416 4059 4773 3337
## NABP1 718 833 909 464 544 847
## SF3B1 4243 5200 5605 5746 4598 5139
## CASP10 385 376 345 364 434 427
## CD28 658 708 884 740 657 503
## CTLA4 75 40 89 90 86 26
## ICOS 135 171 179 130 147 125
## NDUFS1 453 607 575 497 655 583
## CXCR2 18096 20566 19235 14831 12093 25371
## IRS1 93 42 82 71 91 72
## CCL20 7 5 2 4 4 12
## ATG16L1 316 348 368 346 404 290
## GPR35 62 65 114 164 104 122
## PDCD1 50 23 30 18 60 20
## PPARG 8 1 1 5 4 7
## RPL15 13829 12528 12457 18160 17973 13795
## EOMES 134 314 107 51 257 91
## CX3CR1 2331 2381 742 538 1431 1709
## ACKR2 1 2 4 2 1 1
## CCR2 613 712 449 315 470 957
## CCRL2 30 36 54 46 37 36
## TLR9 59 52 80 56 76 76
## ARHGEF3 1199 1364 1376 1071 1506 1027
## ADAMTS9 0 0 0 0 0 0
## TMEM45A 1 0 4 1 1 0
## CD80 15 3 4 5 4 2
## CD86 786 658 918 1128 947 1035
## MIX23 33 33 37 19 40 25
## PLS1 23 26 15 14 26 12
## PTX3 42 62 52 57 42 82
## GOLIM4 85 95 73 76 97 92
## MYNN 300 351 473 372 339 322
## TNFSF10 2554 3460 3864 1373 2058 3132
## ADIPOQ 0 0 0 0 0 0
## SPON2 1042 440 314 392 872 453
## S100P 1812 1905 5396 3323 1587 3690
## WDR1 5241 6255 6498 5101 6057 5688
## CD38 419 299 356 233 436 218
## PPARGC1A 5 0 2 7 8 5
## TMPRSS11B 0 0 0 0 0 0
## CSN3 0 0 0 0 0 0
## ALB 0 0 0 1 0 0
## CXCL8 86428 68609 26530 66279 26599 149192
## CXCL2 29 38 13 26 19 179
## AREG 39 19 31 97 13 24
## CXCL10 24 37 31 16 46 22
## CXCL13 0 1 1 0 1 1
## SPP1 32 13 49 49 49 68
## HERC6 218 148 315 128 206 182
## NFKB1 886 1027 1065 873 912 969
## SEC24B 374 405 547 507 441 452
## EGF 14 18 20 16 14 14
## IL2 0 0 0 0 0 1
## IL21 2 2 0 0 1 0
## IL21-AS1 1 1 0 1 2 0
## SLC7A11 11 10 17 3 10 8
## IL15 76 80 103 57 91 100
## EDNRA 0 0 0 1 0 0
## TLR2 3021 2978 3024 2343 2064 4213
## FGB 0 0 0 0 0 0
## DDX60 354 507 792 186 401 190
## SPCS3 1609 1998 2286 1799 2031 1989
## TLR3 10 19 9 6 18 3
## OSMR 25 16 43 33 17 25
## GZMK 555 509 545 284 1119 324
## GZMA 1346 1296 941 623 2070 618
## ANKRD55 92 140 116 68 145 56
## CENPK 16 15 77 18 28 106
## CAST 2972 2357 2349 2324 2717 2841
## ERAP1 1509 1500 1263 1096 1907 1119
## ERAP2 1535 1809 1585 1363 235 1268
## TNFAIP8 1441 1527 1793 1198 1685 1302
## CSF2 1 0 0 0 0 0
## IL5 0 0 0 0 0 0
## IL13 1 0 0 0 2 0
## IL4 6 9 7 0 1 0
## CD14 7825 6926 8542 10042 8622 11966
## CSNK1A1 1497 1784 1756 1379 1633 1680
## PPARGC1B 131 124 130 142 122 118
## TNIP1 4618 4297 4761 4016 3783 4429
## ATOX1 182 151 205 220 194 195
## FAXDC2 126 176 162 145 121 112
## IL12B 3 1 1 0 0 2
## MIR146A 0 0 0 0 1 0
## PDLIM7 1564 1427 2017 1653 1348 1932
## SERPINB1 4199 3636 4580 4670 4131 5234
## SSR1 2001 2174 2534 2206 2222 2352
## CD83 631 648 712 437 469 965
## SOX4 153 85 122 318 174 148
## CMAHP 41 96 106 69 144 47
## HLA-A 40753 40633 61216 42700 39964 40864
## HLA-C 44667 63359 90590 84364 57073 66543
## HLA-B 76554 113185 124363 119087 97423 84345
## MICA 231 196 121 116 144 157
## LTA 95 98 60 60 120 61
## TNF 162 238 226 408 323 399
## HLA-DRB1 2941 5077 7279 4820 4513 3950
## HLA-DQB1 255 2592 3770 477 838 1416
## PPARD 327 294 368 380 386 309
## CCND3 4184 4264 3708 4234 4170 4208
## VEGFA 158 153 219 217 113 204
## RUNX2 508 368 645 598 422 618
## IL17A 0 0 0 0 0 0
## IL17F 0 0 0 0 0 0
## PRDM1 446 516 469 400 562 449
## ATG5 322 376 493 452 432 355
## TRAF3IP2 186 220 163 229 232 197
## NCOA7 310 313 341 282 364 313
## SGK1 2899 3993 6094 2828 3231 6591
## IFNGR1 2167 2282 3668 2864 2304 2800
## TNFAIP3 3893 4186 2647 5143 2210 9325
## SOD2 38035 36651 51551 46224 26703 37167
## LPAL2 14 17 9 9 25 20
## PLG 1 0 1 1 0 1
## CCR6 121 105 87 96 128 95
## RAC1 2499 2721 2864 2722 2663 3157
## ZNF316 1023 711 807 817 883 585
## AHR 946 621 1389 1033 737 949
## IL6 12 2 2 4 0 2
## TOMM7 2001 1670 1874 1942 1995 2041
## CYCS 774 655 577 520 635 586
## AQP1 5 3 3 2 1 1
## NT5C3A 556 635 945 583 567 555
## EGFR 0 0 0 0 0 1
## CD36 2054 1369 1739 1677 1689 3541
## SAMD9 1956 2562 2442 887 1485 1492
## SERPINE1 10 16 8 11 8 18
## CUX1 1433 1184 1535 1746 1330 1296
## PSMC2 329 395 365 341 455 405
## NAMPT 30331 32360 73409 55636 29997 44135
## HYAL4 0 0 0 0 0 0
## LEP 6 8 6 3 2 3
## CALD1 8 11 24 4 3 6
## BRAF 651 658 736 631 576 547
## EZH2 53 50 81 46 78 60
## DNAJB6 1237 1512 1511 1779 1342 1601
## CSMD1 1 0 34 0 0 2
## CTSB 4713 3925 5649 5576 5213 6681
## EGR3 825 2185 915 299 480 1294
## TNFRSF10A 194 201 185 171 196 167
## BNIP3L 1754 1979 2794 2467 1975 2730
## DUSP4 41 26 55 58 49 57
## NRG1 108 45 107 103 68 323
## RPL7 10503 9359 9691 13341 11971 9422
## IL7 17 10 11 8 16 17
## GEM 0 2 1 0 1 2
## MYC 682 822 813 593 887 690
## GPT 5 1 4 1 3 1
## JAK2 937 805 995 604 795 979
## CD274 126 199 182 101 133 169
## IL33 0 0 0 0 0 0
## LURAP1L-AS1 0 0 0 0 0 0
## LURAP1L 0 2 1 1 1 0
## TTC39B 179 223 196 129 191 139
## IFNA1 0 0 0 0 0 0
## TEK 8 18 19 15 32 20
## TRBV20OR9-2 0 0 0 0 0 0
## TOMM5 239 243 205 206 266 193
## ANXA1 5767 4384 6561 7746 6869 7084
## ERP44 1138 1218 1564 1304 1354 1305
## ZNF483 33 49 35 26 35 21
## TNFSF15 8 7 6 1 6 2
## TLR4 5126 6306 7582 4028 3883 5117
## PTGS1 531 666 1061 631 473 424
## HSPA5 6985 7850 6225 5102 4159 10847
## FNBP1 2967 3396 3699 3549 3828 3365
## CARD9 212 129 152 147 193 228
## TRAF2 153 174 145 131 167 136
## CLIC3 189 121 79 132 258 111
## IL2RA 124 81 120 66 109 74
## GATA3 387 432 346 264 439 406
## VIM 15150 13125 15177 16488 17169 21654
## CREM 139 134 192 253 138 121
## DKK1 0 0 0 0 0 0
## MBL2 0 0 0 0 0 0
## SAR1A 669 723 1218 1041 887 776
## PRF1 3511 3838 2368 1826 5550 1564
## ZMIZ1 2144 1558 2120 2562 1917 2075
## IFIT3 3353 4789 12052 1658 2519 2440
## TALDO1 8076 8102 11132 9449 8190 11454
## IGF2 0 0 1 0 0 0
## INS-IGF2 0 0 1 0 0 0
## IGF2-AS 0 0 0 0 0 0
## INS 0 0 0 0 0 0
## STIM1 1278 1379 1336 1393 1400 1240
## TRIM22 2006 2761 3500 1796 2693 1977
## PTH 0 0 0 0 0 0
## SAA1 0 0 0 0 1 1
## SLC1A2 2 3 1 1 0 1
## FOSL1 42 27 82 47 23 73
## CCND1 9 11 13 6 9 3
## JRKL 113 128 86 57 101 102
## MMP7 1 0 0 0 0 0
## MMP1 1 1 2 0 0 3
## MMP3 0 0 0 0 0 0
## CASP1 2352 2523 3008 2513 2723 3048
## DLAT 202 230 199 156 279 223
## IL18 97 68 77 122 97 79
## CD3E 3339 4032 3433 3081 4890 2223
## MCAM 230 239 282 245 204 168
## WNK1 3523 4183 3274 2939 3482 3492
## TNFRSF1A 3126 3068 4285 2674 2921 3869
## GAPDH 14617 14151 16104 21197 18042 19713
## CD4 3235 3156 4439 5020 4492 5016
## SLC2A3 8489 7734 13576 9966 6135 8405
## CLEC4D 174 424 364 262 153 288
## KLRB1 1016 559 857 904 1674 647
## CD69 3131 3235 1860 1646 1708 3387
## CLEC2B 1359 1664 1967 1577 1583 1741
## OLR1 2 16 7 10 11 77
## ABCD2 173 243 251 154 226 153
## LRRK2 6394 7042 7446 6423 4586 6563
## VDR 353 432 476 386 374 383
## TMBIM6 12150 13397 15019 12233 13472 13572
## PFDN5 3367 2979 3301 4599 4432 3430
## SP7 0 0 1 0 1 0
## MUCL1 0 1 0 0 0 0
## CD63 2358 2310 2952 3125 2757 3093
## SUOX 868 1051 1227 942 1174 1011
## RPS26 3734 3414 762 8181 1017 3398
## RPL41 7883 7325 7090 9574 9590 7185
## IL23A 55 53 52 49 48 39
## DDIT3 617 585 806 798 436 949
## IFNG 78 76 23 18 73 89
## IL22 1 1 0 0 0 0
## LYZ 44429 77805 69418 90564 70541 95311
## CAPS2 5 8 10 4 4 7
## SYT1 3 1 1 0 6 1
## BTG1 9541 11025 10276 10904 9613 11145
## HCAR3 3630 3483 2386 1643 1841 3511
## GJB2 1 0 3 6 1 1
## GJB6 26 10 43 39 12 17
## TNFSF11 4 2 5 4 1 0
## TPT1 53226 47553 55228 74936 68105 57079
## LMO7 82 109 87 80 108 68
## TNFSF13B 1925 1593 3459 2495 1639 2178
## LAMP1 2695 2824 3227 2646 3112 2806
## PSME2 1221 1413 1609 1565 1822 1119
## GZMB 1374 835 551 1057 1337 546
## RPL36AL 2195 2197 2595 2350 2425 1617
## PYGL 4055 4364 6475 4920 3715 5540
## HIF1A 1738 1709 3821 3659 1573 1773
## FOS 89861 55929 33126 63782 37029 61814
## JDP2 598 611 854 884 662 860
## NOXRED1 11 8 6 5 5 6
## SERPINA1 20937 20812 25612 22967 16486 27542
## CDC42BPB 220 157 179 285 230 317
## PLA2G4D 0 0 0 0 0 0
## TRIM69 13 22 17 10 18 10
## SLC51B 0 0 0 0 0 0
## SMAD3 681 539 657 669 819 528
## CYP1A1 1 1 1 0 2 3
## AKAP13 3551 4597 4066 4005 3684 2750
## MEFV 2052 2365 2997 2419 2375 3192
## SOCS1 112 83 89 42 60 34
## ATXN2L 1950 2023 1864 1878 2316 1967
## CD19 258 145 83 115 209 93
## ITGAL 5475 6418 5300 4180 6253 5493
## ITGAM 4343 4701 5653 4722 3813 4585
## ITGAX 4744 3887 5658 5786 4309 5621
## DNAJA2 547 718 716 589 750 777
## SIAH1 99 121 154 166 130 110
## ADCY7 2930 2412 1991 2056 2593 2305
## NOD2 414 464 470 433 677 494
## CMTM2 2158 1902 3113 2095 2001 2343
## SF3B3 863 1240 982 710 1160 978
## PSMD7 660 631 798 849 700 647
## WWOX 31 41 40 66 61 51
## MAF 457 598 473 289 512 391
## SLC7A5 213 221 269 380 255 160
## CXCL16 2069 1399 2023 3345 1712 2435
## XAF1 845 1042 1504 554 991 543
## CD68 3098 3212 3502 5177 4572 4983
## PER1 488 390 729 1401 502 532
## NOS2 2 0 0 7 0 5
## TRAF4 130 120 75 138 152 83
## CCL2 21 29 47 7 28 9
## CCL5 3322 4942 2836 2378 6028 1531
## CCL3 423 556 164 377 303 1749
## CCR7 1143 1376 1020 863 1423 716
## STAT3 3586 5080 5528 4393 3700 4702
## SOST 0 0 0 0 0 0
## ITGA2B 190 423 609 183 85 220
## EFCAB13 26 26 12 22 17 18
## NPEPPS 712 895 934 762 858 963
## TBX21 487 571 255 289 595 255
## COL1A1 1 2 1 0 3 1
## MRPS23 180 179 169 167 252 178
## MIR21 2 4 10 7 5 3
## RPS6KB1 368 380 366 321 446 329
## ACE 44 42 46 48 37 20
## ERN1 822 1074 1554 1348 1340 976
## PRTN3 9 6 0 3 9 30
## PLIN5 105 70 144 116 72 121
## RETN 53 66 24 69 84 142
## CCL25 0 1 0 0 0 0
## ICAM1 1679 1279 2040 2404 1457 2131
## TYK2 1858 1867 1956 1770 1990 2288
## SMARCA4 821 802 638 656 847 757
## ACP5 256 359 169 369 300 211
## JUNB 40161 26651 38192 49607 34696 50002
## CYP4F22 51 66 23 20 57 41
## JAK3 1851 1899 2191 2072 1698 2103
## JUND 17105 8939 5781 7163 7401 9792
## CEBPA 749 612 766 1050 848 797
## CEBPG 246 278 261 279 298 325
## ACP7 0 1 0 1 0 2
## ZFP36 30462 23969 31430 39018 20574 81946
## TGFB1 5006 4136 5128 4911 6176 5393
## RPS19 11690 10230 9196 11642 13321 9574
## PSG2 0 0 0 0 0 0
## FUT2 6 1 4 3 2 3
## NKG7 4447 4783 2466 2588 6018 2319
## ZNF415 6 6 6 12 22 1
## LILRB2 5193 3686 4865 4468 4225 5267
## LILRA5 2906 2264 2800 1771 2853 2995
## KIR3DL1 143 4 31 281 59 54
## KIR3DL2 118 19 44 28 78 9
## SMOX 71 93 114 94 57 65
## BMP2 6 9 6 4 1 8
## GINS1 7 10 16 10 12 6
## PLCG1 934 1052 999 889 1154 849
## YWHAB 5473 5924 6703 5522 6079 5922
## PI3 1034 688 580 863 822 1480
## MMP9 1240 3027 2280 1336 2044 2225
## CD40 216 138 129 138 305 119
## PFDN4 53 45 49 66 61 59
## BMP7 0 0 0 0 0 0
## RPS21 5047 4763 4347 6234 6371 4775
## MX1 1106 850 3861 622 1061 519
## PFKL 1293 1195 1125 1198 1344 1432
## IL17RA 4963 4853 5317 4635 4253 4513
## UBE2L3 960 1076 1125 962 1189 1077
## TPST2 1417 1105 1037 871 1438 1187
## XBP1 827 1113 1133 1069 1211 979
## UQCR10 544 536 533 572 676 582
## SEC14L2 66 30 52 56 24 36
## APOL6 1238 2454 1685 1062 1311 1090
## APOL1 572 914 900 483 665 488
## TYMP 2862 2864 2979 3007 3648 4283
## BEND2 18 67 64 38 24 39
## PHEX 7 13 15 14 17 6
## TIMP1 1228 1201 1330 1791 1659 1239
## FOXP3 86 76 101 91 92 58
## MSN 20915 24110 26981 23939 24167 25502
## PGK1 6735 6380 8424 8628 7214 8132
## LAMP2 5289 6149 8736 6100 5262 7156
## CD40LG 188 341 167 119 243 217
## IRAK1 1488 1303 1329 1498 1529 1268
## COX2 62507 47099 49513 76405 69573 43619
## GSM3308540 GSM3308541 GSM3308542 GSM3308543 GSM3308544
## TNFRSF9 149 119 138 91 71
## ENO1 8082 6185 4198 6697 5843
## PIK3CD 6555 6861 4961 5293 5306
## PGD 7592 4594 3824 3656 3689
## MTHFR 399 665 299 399 354
## TNFRSF1B 18265 13258 10760 11125 14567
## PINK1 648 711 386 547 733
## IFNLR1 34 71 42 112 62
## RUNX3 3568 3987 2381 4812 4413
## SH3BGRL3 12382 9825 7460 9860 12493
## CD52 4251 4285 1896 5050 4696
## IFI6 1041 836 18406 807 1644
## ZC3H12A 605 343 1077 667 1324
## UTP11 115 112 94 117 78
## JUN 6473 6316 3791 27941 29549
## KANK4 0 0 0 0 0
## EFCAB7 17 31 18 36 16
## IL23R 0 3 0 8 9
## ADGRL2 0 0 1 0 0
## GBP3 133 176 443 212 74
## GBP1 770 713 8455 693 753
## GBP5 2370 1932 15479 2452 2791
## TGFBR3 649 700 449 972 1049
## VCAM1 0 4 0 6 1
## PTPN22 445 464 227 424 213
## CD160 137 166 74 185 130
## FCGR1A 1122 365 2103 405 957
## MCL1 21964 17933 43302 20044 27363
## CTSK 73 67 61 44 49
## RORC 27 59 21 82 64
## S100A9 133352 80372 137617 74733 121556
## S100A12 3843 1977 4829 1642 2694
## S100A8 48649 27959 54159 28840 46880
## IL6R 4431 3548 2712 2745 3827
## RIT1 1517 1033 872 1053 1372
## BGLAP 9 6 4 6 8
## IFI16 2206 2611 11229 2053 1242
## AIM2 103 79 581 71 65
## CRP 0 0 0 0 0
## FCGR2A 11590 11027 16116 8629 9486
## HSPA6 1683 1872 1932 2105 911
## FCGR3A 13062 11225 19621 11789 14426
## SELL 40912 24719 46185 26471 22038
## GLUL 19628 14826 23969 11619 16996
## PTGS2 1503 3056 38941 21162 8863
## CRB1 0 0 0 3 1
## KDM5B 407 408 218 400 450
## IL10 13 4 16 5 4
## YOD1 318 244 148 224 227
## HHAT 35 46 26 75 48
## TRAF5 283 493 175 444 294
## NLRP3 919 662 2155 827 1121
## LINC01250 0 0 0 0 0
## RPS7 9128 10047 4520 9744 9566
## RSAD2 316 202 25652 252 353
## FOSL2 2964 2969 3673 3046 6409
## REL 1290 1078 786 1124 1020
## TGFA 446 376 496 326 499
## DYSF 4344 2515 7757 2501 3344
## HK2 1087 710 963 908 888
## CD8A 603 1804 1168 3399 1755
## CD8B 238 644 491 1296 690
## EIF5B 487 514 289 593 390
## IL1R1 203 257 272 135 222
## RGPD6 103 93 48 93 65
## IL1A 0 0 16 8 1
## IL1B 471 459 10913 2691 1321
## IL37 0 0 0 0 0
## IL36RN 0 0 0 0 0
## IL1F10 0 0 0 0 0
## IL1RN 1879 1632 48817 3704 4845
## NMI 1649 1331 3758 938 954
## TNFAIP6 263 259 2585 381 176
## IFIH1 323 288 3603 379 351
## SCN1A 0 0 0 0 0
## ABCB11 0 2 3 0 0
## RBM45 62 86 42 63 47
## FRZB 0 0 0 0 0
## TFPI 5 4 2 2 5
## STAT1 4070 3749 12872 4511 2592
## NABP1 561 565 1317 675 384
## SF3B1 5433 4549 4881 4658 3636
## CASP10 368 349 555 341 268
## CD28 730 852 324 1015 590
## CTLA4 100 109 104 101 57
## ICOS 152 152 272 186 122
## NDUFS1 558 561 422 579 374
## CXCR2 18872 17158 21640 12622 13087
## IRS1 61 86 44 60 69
## CCL20 0 2 12 25 23
## ATG16L1 311 425 189 428 334
## GPR35 108 108 101 75 142
## PDCD1 35 76 37 72 52
## PPARG 5 2 0 4 0
## RPL15 15033 16085 8137 15291 14986
## EOMES 70 156 95 196 112
## CX3CR1 932 1064 665 1159 517
## ACKR2 2 2 0 2 0
## CCR2 1102 712 477 476 386
## CCRL2 77 33 65 57 39
## TLR9 71 73 41 44 45
## ARHGEF3 1181 1216 934 1808 887
## ADAMTS9 0 0 0 0 0
## TMEM45A 0 1 1 1 2
## CD80 3 7 9 4 1
## CD86 1011 944 841 699 890
## MIX23 29 34 14 37 19
## PLS1 23 19 13 24 20
## PTX3 155 33 134 72 134
## GOLIM4 95 87 60 53 62
## MYNN 338 308 257 365 370
## TNFSF10 1829 2235 26922 1568 1423
## ADIPOQ 0 0 0 0 0
## SPON2 535 555 373 352 434
## S100P 3206 1743 1350 2347 3638
## WDR1 5874 5764 4190 5757 4676
## CD38 281 246 347 199 141
## PPARGC1A 0 7 2 1 1
## TMPRSS11B 0 0 0 0 0
## CSN3 0 0 0 0 0
## ALB 0 0 0 0 0
## CXCL8 25141 27756 39295 99946 99361
## CXCL2 12 10 64 56 25
## AREG 270 10 140 82 108
## CXCL10 22 10 1193 20 16
## CXCL13 0 0 0 2 0
## SPP1 20 29 31 13 181
## HERC6 182 189 1002 229 113
## NFKB1 1349 1009 791 1001 708
## SEC24B 568 459 370 509 353
## EGF 28 19 16 21 12
## IL2 3 3 0 1 1
## IL21 0 3 1 1 0
## IL21-AS1 1 3 1 0 1
## SLC7A11 22 9 13 14 4
## IL15 87 84 111 75 64
## EDNRA 0 0 0 0 0
## TLR2 4868 2389 3816 2677 2931
## FGB 0 0 0 0 0
## DDX60 301 320 2750 396 264
## SPCS3 2175 1950 1733 1874 1802
## TLR3 8 12 19 15 18
## OSMR 26 19 39 27 25
## GZMK 303 1071 387 1646 1446
## GZMA 844 1235 896 1716 1344
## ANKRD55 129 26 55 63 32
## CENPK 12 25 6 97 42
## CAST 2724 3198 2061 2543 2037
## ERAP1 1272 1974 1124 1315 1006
## ERAP2 1552 1409 2366 1751 151
## TNFAIP8 1357 1568 752 1746 1096
## CSF2 0 0 1 0 3
## IL5 2 1 2 0 0
## IL13 0 0 2 0 1
## IL4 6 7 9 8 3
## CD14 12481 7501 9807 7185 10441
## CSNK1A1 1618 1615 1344 1533 1268
## PPARGC1B 174 151 83 121 104
## TNIP1 4803 4086 3311 3872 3660
## ATOX1 216 149 141 186 215
## FAXDC2 163 133 102 150 99
## IL12B 0 0 1 2 0
## MIR146A 0 1 0 1 0
## PDLIM7 1896 1759 1553 1256 1716
## SERPINB1 5576 3965 9708 3532 3575
## SSR1 2481 2084 1758 2187 2165
## CD83 456 370 2409 1064 1000
## SOX4 254 189 121 234 184
## CMAHP 93 90 80 90 58
## HLA-A 41672 43032 47586 45019 58520
## HLA-C 107225 67329 92397 84059 87157
## HLA-B 135204 92955 126018 101144 127352
## MICA 112 110 118 160 111
## LTA 55 83 22 77 57
## TNF 358 254 380 423 388
## HLA-DRB1 4163 7194 7090 4411 8029
## HLA-DQB1 240 3980 3987 689 1989
## PPARD 411 470 157 342 292
## CCND3 5541 3845 4112 4273 3633
## VEGFA 126 161 210 216 258
## RUNX2 602 581 203 551 532
## IL17A 0 0 0 0 1
## IL17F 0 0 0 0 0
## PRDM1 612 511 760 652 604
## ATG5 487 370 320 519 398
## TRAF3IP2 214 219 109 206 168
## NCOA7 358 387 1481 369 340
## SGK1 3096 3145 3879 5397 5366
## IFNGR1 4452 2747 2129 2048 1627
## TNFAIP3 4595 2169 24118 17842 13365
## SOD2 40485 31820 58572 26143 40440
## LPAL2 12 21 14 17 13
## PLG 0 1 2 0 1
## CCR6 115 95 54 124 79
## RAC1 3136 2332 2047 2281 2494
## ZNF316 883 1029 662 882 740
## AHR 1823 1032 1219 1342 1483
## IL6 1 1 32 16 15
## TOMM7 2306 2242 1299 2803 2212
## CYCS 592 541 739 1046 746
## AQP1 2 3 1 1 2
## NT5C3A 598 593 2603 530 470
## EGFR 0 0 0 0 0
## CD36 3734 1800 1821 1851 1827
## SAMD9 999 1275 8060 1472 941
## SERPINE1 4 6 10 13 8
## CUX1 1695 1448 1270 1376 1876
## PSMC2 436 441 251 434 266
## NAMPT 64785 35240 51752 36240 45918
## HYAL4 0 1 0 0 0
## LEP 5 8 1 4 1
## CALD1 10 2 4 8 2
## BRAF 640 639 395 655 546
## EZH2 60 91 45 60 42
## DNAJB6 1587 1354 1440 1357 1586
## CSMD1 31 7 2 1 44
## CTSB 7621 6293 5452 4905 9381
## EGR3 462 376 2011 879 640
## TNFRSF10A 194 229 118 213 143
## BNIP3L 2295 2018 2703 1812 1772
## DUSP4 47 70 73 126 81
## NRG1 150 29 25 87 100
## RPL7 10752 10980 5269 11063 10967
## IL7 6 10 13 29 9
## GEM 0 2 2 3 2
## MYC 895 733 284 677 438
## GPT 1 1 3 0 4
## JAK2 1198 700 1376 828 676
## CD274 219 120 1007 81 94
## IL33 0 1 0 0 0
## LURAP1L-AS1 0 0 0 0 0
## LURAP1L 0 0 0 0 1
## TTC39B 157 165 154 169 102
## IFNA1 0 0 0 0 0
## TEK 13 14 12 37 25
## TRBV20OR9-2 0 0 0 0 0
## TOMM5 211 257 137 230 219
## ANXA1 10630 7868 9352 6105 6990
## ERP44 1563 1200 1507 1238 1393
## ZNF483 37 32 13 43 17
## TNFSF15 3 8 9 2 7
## TLR4 5726 3486 7468 3041 5384
## PTGS1 863 624 409 574 548
## HSPA5 6339 4338 18592 7409 7498
## FNBP1 3293 3962 2552 3537 2580
## CARD9 186 161 147 160 169
## TRAF2 122 172 74 155 91
## CLIC3 169 166 93 108 123
## IL2RA 202 155 31 103 62
## GATA3 231 477 293 632 253
## VIM 19868 16699 14247 14580 17957
## CREM 228 163 243 205 270
## DKK1 0 0 0 0 0
## MBL2 0 0 0 0 0
## SAR1A 1003 809 654 807 882
## PRF1 2946 2717 1605 2214 1594
## ZMIZ1 3337 2129 1465 1916 2521
## IFIT3 2497 2070 107804 2637 3322
## TALDO1 9376 8097 8591 7051 8695
## IGF2 0 0 0 0 0
## INS-IGF2 0 0 0 0 0
## IGF2-AS 0 0 0 0 0
## INS 0 0 0 0 0
## STIM1 1447 1401 844 1360 1118
## TRIM22 2316 2139 12338 1930 1656
## PTH 0 0 0 0 1
## SAA1 0 0 0 0 0
## SLC1A2 3 0 3 0 1
## FOSL1 44 19 125 78 156
## CCND1 13 4 8 8 9
## JRKL 46 108 41 85 52
## MMP7 0 0 0 0 0
## MMP1 2 0 3 1 0
## MMP3 0 0 0 0 0
## CASP1 3121 2340 5848 2205 2098
## DLAT 176 222 123 234 158
## IL18 177 104 49 77 96
## CD3E 2750 3460 1807 4600 3807
## MCAM 288 231 153 226 177
## WNK1 3550 3374 1875 4062 2951
## TNFRSF1A 3341 3256 3437 2237 2800
## GAPDH 21284 17676 15229 16404 20486
## CD4 5056 4647 3238 4915 3749
## SLC2A3 8057 7376 10384 8319 9222
## CLEC4D 276 242 851 180 177
## KLRB1 595 993 339 1157 1778
## CD69 1062 1299 10880 8343 3560
## CLEC2B 1758 1474 2868 1540 1458
## OLR1 37 12 7 7 8
## ABCD2 123 190 67 292 107
## LRRK2 5003 4682 8894 4701 5065
## VDR 472 335 398 301 314
## TMBIM6 13688 12580 10878 12024 13470
## PFDN5 3692 3578 2403 3483 3803
## SP7 0 0 0 1 1
## MUCL1 0 0 0 1 0
## CD63 3846 2888 2244 2267 3317
## SUOX 990 1106 646 935 796
## RPS26 6762 3986 575 758 828
## RPL41 7801 8916 4498 8700 8523
## IL23A 43 57 56 70 57
## DDIT3 484 509 504 661 563
## IFNG 18 37 200 189 91
## IL22 0 2 0 0 0
## LYZ 52254 104121 125862 30869 96513
## CAPS2 10 5 2 5 5
## SYT1 3 9 0 4 4
## BTG1 10815 8590 7913 13333 11846
## HCAR3 1560 1626 3180 3128 1915
## GJB2 0 0 2 0 3
## GJB6 21 23 8 9 33
## TNFSF11 7 2 0 1 4
## TPT1 60558 52623 35061 58646 66369
## LMO7 98 55 30 87 49
## TNFSF13B 1717 2244 11904 1411 2159
## LAMP1 3621 2968 2560 2687 3125
## PSME2 1532 1163 2655 1330 1330
## GZMB 982 1018 829 832 889
## RPL36AL 2362 2312 1492 2660 2677
## PYGL 5421 3492 4105 3048 3483
## HIF1A 4746 2026 3373 2331 2975
## FOS 51318 38870 61969 52731 66171
## JDP2 1031 572 606 519 934
## NOXRED1 7 8 1 9 2
## SERPINA1 27328 14427 29819 17094 23425
## CDC42BPB 180 306 149 225 246
## PLA2G4D 0 0 0 0 0
## TRIM69 12 29 21 12 14
## SLC51B 0 0 0 0 0
## SMAD3 770 893 563 831 616
## CYP1A1 0 0 1 0 1
## AKAP13 4745 3966 3564 4260 3975
## MEFV 2635 2975 3648 1735 1938
## SOCS1 101 78 393 130 90
## ATXN2L 1738 2193 1165 2224 1486
## CD19 59 243 77 168 146
## ITGAL 6008 4895 3830 6501 4931
## ITGAM 5856 3733 4144 3362 5318
## ITGAX 6965 3353 6770 3060 4825
## DNAJA2 669 725 458 634 601
## SIAH1 176 155 77 138 100
## ADCY7 2066 2679 2923 2065 2242
## NOD2 597 469 1402 601 1178
## CMTM2 2040 1370 1848 1433 2439
## SF3B3 756 995 463 1317 637
## PSMD7 928 730 474 692 654
## WWOX 44 64 25 58 57
## MAF 455 753 288 695 372
## SLC7A5 294 404 294 257 583
## CXCL16 2356 1782 2164 2371 2849
## XAF1 785 627 5515 751 715
## CD68 6305 3668 5046 3422 4187
## PER1 2045 596 726 992 1625
## NOS2 3 3 0 2 0
## TRAF4 111 133 142 145 149
## CCL2 19 13 608 15 17
## CCL5 2251 4549 2412 6977 4794
## CCL3 309 284 980 700 257
## CCR7 1419 679 558 645 514
## STAT3 4670 4538 4800 3720 2982
## SOST 0 0 0 0 0
## ITGA2B 547 172 164 245 165
## EFCAB13 31 25 17 23 18
## NPEPPS 882 876 707 658 605
## TBX21 264 437 264 688 338
## COL1A1 0 0 2 1 0
## MRPS23 166 205 129 174 104
## MIR21 6 5 8 6 6
## RPS6KB1 429 409 237 393 332
## ACE 30 116 18 90 39
## ERN1 1318 1550 730 1266 1293
## PRTN3 19 13 1 3 3
## PLIN5 97 87 181 57 84
## RETN 125 53 52 64 48
## CCL25 0 0 1 0 0
## ICAM1 2590 1415 2807 1589 2479
## TYK2 1642 2096 1584 1265 1149
## SMARCA4 751 797 458 799 588
## ACP5 249 272 128 226 351
## JUNB 43540 37142 43426 47541 43263
## CYP4F22 102 19 24 60 77
## JAK3 2276 1798 2642 1502 1334
## JUND 6810 5298 13026 14785 17471
## CEBPA 1099 918 445 632 986
## CEBPG 332 332 235 308 284
## ACP7 0 2 0 0 1
## ZFP36 28362 19512 57686 60587 36305
## TGFB1 6031 5286 6535 5285 5869
## RPS19 10573 13131 5692 12367 11677
## PSG2 0 0 0 0 0
## FUT2 5 3 1 3 4
## NKG7 3180 3991 2639 5558 4673
## ZNF415 6 17 6 3 6
## LILRB2 6847 3699 5431 3221 4295
## LILRA5 3618 1797 5797 1129 1841
## KIR3DL1 74 174 32 91 80
## KIR3DL2 41 72 13 60 38
## SMOX 63 67 52 69 76
## BMP2 15 2 3 4 7
## GINS1 8 12 2 9 6
## PLCG1 879 1006 407 988 511
## YWHAB 6272 5643 4304 5707 5807
## PI3 4176 318 1099 1719 616
## MMP9 1300 1635 1743 1094 2417
## CD40 121 188 186 139 124
## PFDN4 58 56 22 58 55
## BMP7 0 0 0 0 0
## RPS21 4985 5627 2651 5861 5134
## MX1 894 1023 22494 798 714
## PFKL 1155 1500 944 1362 1111
## IL17RA 4848 4600 4744 3405 3984
## UBE2L3 1149 1085 829 1028 831
## TPST2 1221 1187 870 1351 1107
## XBP1 1374 1328 1224 1168 1141
## UQCR10 607 579 403 547 553
## SEC14L2 33 29 30 37 58
## APOL6 1313 1244 9473 1387 1128
## APOL1 614 689 2813 480 602
## TYMP 3129 3970 10365 2295 3750
## BEND2 30 15 16 41 19
## PHEX 12 30 4 11 8
## TIMP1 1663 1901 1301 1107 1608
## FOXP3 73 126 34 121 60
## MSN 24991 19362 17699 23964 24816
## PGK1 9233 6819 6791 6786 8622
## LAMP2 6844 5653 5822 4881 6375
## CD40LG 171 196 90 231 154
## IRAK1 1726 1773 1169 1480 1858
## COX2 63637 53347 33759 51838 687334. Selection of samples
Selection of samples related to psoriatic arthritis and ankylosing spondylitis from the dataset
# sample selection
gsms <- "22222222222222222222222XXXXXXXXXXXXXXXXXXXXXXXXXXX1X0XX0001011011XXXX00XXXXXXXXXXXXXXXX0XX11022222222222222222222222222"
sml <- strsplit(gsms, split="")[[1]]
# Filter out excluded samples (marked as "X")
sel <- which(sml != "X")
sml <- sml[sel]
expr_data <- expr_data_filtered[, sel]
# group membership for samples
gs <- factor(sml)
groups <- make.names(c("PsA", "AS", "Healthy"))
levels(gs) <- groups
sample_info <- data.frame(Group = gs, row.names = colnames(expr_data))
dsa <- DESeqDataSetFromMatrix(countData=expr_data, colData=sample_info, design= ~Group)
dsb <- DESeq(dsa, test="LRT", reduced = ~ 1) # Use LRT for all-around gene ranking## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing## -- replacing outliers and refitting for 11 genes
## -- DESeq argument 'minReplicatesForReplace' = 7
## -- original counts are preserved in counts(dds)## estimating dispersions## fitting model and testing# extract results for top genes table
r <- results(dsb, alpha=0.05, pAdjustMethod ="fdr")
plotDispEsts(dsb, main="GSE117769 Dispersion Estimates")
# create histogram plot of p-values
hist(r$padj, breaks=seq(0, 1, length = 21), col = "grey", border = "white",
xlab = "", ylab = "", main = "GSE117769 Frequencies of padj-values")
#Depois de filtrar quais os grupos apresentam algum genes expressos
cts <- list(c("Group",groups[1],groups[3]),
c("Group",groups[2],groups[3]),
c("Group",groups[2],groups[1])) # contrasts of interest
# Wald test to obtain contrast-specific results
dsc <- DESeq(dsa, test = "Wald", sfType = "poscount")## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing## -- replacing outliers and refitting for 9 genes
## -- DESeq argument 'minReplicatesForReplace' = 7
## -- original counts are preserved in counts(dds)## estimating dispersions## fitting model and testingr <- results (dsc, contrast=cts[[1]], alpha=0.05, pAdjustMethod = "fdr")
# Venn diagram
library(gplots)
all_res <- list()
for (ct in cts) {
i <- length(all_res)
r <- results(dsc, contrast=ct, alpha=0.05, pAdjustMethod = "fdr")
all_res[[i + 1]] <- rownames(r)[!is.na(r$padj) & r$padj < 0.05 & abs(r$log2FoldChange) >= 1.0 ]
names(all_res)[i + 1] <- paste(ct, collapse="_")
}
venn(all_res)
5. Differential gene expression analysis
# Differential gene expression analysis
df <- as.data.frame(r)
df <- na.omit(df)
topGenes <- rownames(df)
heatmapData <- expr_data[topGenes, ]
# Load the necessary libraries
library(pheatmap)
library(RColorBrewer)
# Calculate the average expression for each gene
media_dos_genes <- rowMeans(heatmapData)
# Sort the averages in descending order
media_ordenada <- sort(media_dos_genes, decreasing = TRUE)
# Get the names of the first 20 genes
top_20_genes_por_media <- names(head(media_ordenada, 20))
# Filter the original matrix to keep only the 20 selected genes
heatmapData_top20 <- heatmapData[top_20_genes_por_media, ]
# Create column annotation with groups
annotation_data <- data.frame(
group = sample_info$Group,
row.names = rownames(sample_info)
)
# Reorder columns by group
ordem_grupo <- order(annotation_data$group) # Sort by group name (alphabetical)
heatmapData_top20 <- heatmapData_top20[, ordem_grupo]
annotation_data <- annotation_data[ordem_grupo, , drop = FALSE]
library(ComplexHeatmap)
library(circlize)
# Matrix of the 20 genes
mat <- heatmapData_top20
# Reschedule by line
mat_scaled <- t(scale(t(mat)))
# Create group annotation
ha_col <- HeatmapAnnotation(
Group = annotation_data$group,
col = list(Group = c("PsA" = "#d62728",
"AS" = "#1f77b4",
"Healthy" = "yellow"))
)
# Inverted RdBu color palette
cores <- colorRamp2(c(-2, 0, 2), rev(RColorBrewer::brewer.pal(3, "RdBu")))
# Heatmap with clustering within groups
Heatmap(
mat_scaled,
name = "Z-score",
top_annotation = ha_col,
col = cores,
cluster_columns = TRUE,
cluster_column_slices = TRUE, # << cluster within each group
column_split = annotation_data$group, # << separate the columns by group
cluster_rows = TRUE,
show_column_names = FALSE,
show_row_names = TRUE,
column_title = "Heatmap of the 20 most highly expressed genes (average) from GSE117769",
heatmap_legend_param = list(title = "Z-score")
)
# UMAP plot (multi-dimensional scaling)
expr_data_umap <- expr_data[rowSums(expr_data) > 0, ] # Remove rows with zero sum
u <- umap(t(expr_data_umap), n_neighbors=15, random_state=123)
plot(u$layout, main="GSE186063 UMAP", xlab="", ylab="", tcl=0.1, pch=19, col="blue")
text(u$layout, labels=colnames(expr_data_umap), cex=0.7, pos=3)
# Assuming that rownames(df) are gene symbols
gene_symbols <- rownames(df)
# Convert gene symbols to Entrez IDs
gene_entrez_ids <- bitr(gene_symbols, fromType = "SYMBOL", toType = "ENTREZID", OrgDb = org.Hs.eg.db)## 'select()' returned 1:1 mapping between keys and columns# First, convert the rownames from df into a column
df$Symbol <- rownames(df)
# Perform the join between the original table and the converted IDs
dfd <- merge(df, gene_entrez_ids, by.x = "Symbol", by.y = "SYMBOL", all.x = TRUE)
# Ensure unique symbols
dfd <- dfd[!duplicated(dfd$ENTREZID), ]6. Comparison between peripheral blood samples from PsA patients and control samples.
# Wald test to obtain contrast-specific results
dsd <- DESeq(dsa, test = "Wald", sfType = "poscount")## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing## -- replacing outliers and refitting for 9 genes
## -- DESeq argument 'minReplicatesForReplace' = 7
## -- original counts are preserved in counts(dds)## estimating dispersions## fitting model and testingr <- results(dsd, contrast = c("Group", groups[1], groups[3]), alpha = 0.05, pAdjustMethod = "fdr")
# Filter only significant genes
sig_genes <- subset(r, padj < 0.05 & abs(log2FoldChange) >= 1)
# volcano plot
old.pal <- palette(c("#00BFFF", "#FF3030")) # low-hi colors
par(mar=c(4,4,2,1), cex.main=1.5)
with(sig_genes, {
plot(log2FoldChange, -log10(padj), main=paste(groups[1], "vs", groups[3]),
xlab="log2FC", ylab="-log10(Padj)", pch=20, cex=0.5)
text(log2FoldChange, -log10(padj), labels=rownames(r), cex=0.6, pos=4)
})
with(subset(r, padj<0.05 & abs(log2FoldChange) >= 1),
points(log2FoldChange, -log10(padj), pch=20, col=(sign(log2FoldChange) + 3)/2, cex=1))
legend("bottomleft", title=paste("Padj<", 0.05, sep=""), legend=c("down", "up"), pch=20,col=1:2)
# Plot only significant genes
#MD PLOT
par(mar=c(4,4,2,1), cex.main=1.5)
with(sig_genes, {
plot(log10(baseMean), log2FoldChange,
main=paste(groups[1], "vs", groups[3]),
xlab="log10(mean of normalized counts)", ylab="log2FoldChange",
pch=20, col=(sign(log2FoldChange) + 3)/2, cex=1)
text(log10(baseMean), log2FoldChange, labels=rownames(sig_genes), cex=0.6, pos=4)
})
legend("bottomleft", title=paste("Padj<", 0.05, sep=""), legend=c("down", "up"), pch=20, col=1:2)
abline(h=0)
palette(old.pal) # restaurar paleta
# Add the gene symbols to the points on the graph.
library(ggplot2)
library(ggrepel)
plotVolcano <- function(res, title = "Volcano Plot") {
res$group <- "NS"
res$group[res$padj < 0.05 & res$log2FoldChange > 1] <- "Up"
res$group[res$padj < 0.05 & res$log2FoldChange < -1] <- "Down"
res$label <- ifelse(res$group != "NS", rownames(res), NA)
ggplot(res, aes(x = log2FoldChange, y = -log10(padj), color = group)) +
geom_point(alpha = 0.7, size = 2) +
geom_hline(yintercept = -log10(0.05), linetype = "dashed") +
geom_vline(xintercept = c(-1, 1), linetype = "dashed") +
scale_color_manual(values = c("Up" = "firebrick", "Down" = "dodgerblue", "NS" = "grey80")) +
ggrepel::geom_text_repel(aes(label = label), size = 3, max.overlaps = Inf) +
theme_minimal() +
labs(title = title, x = "log2 Fold Change", y = "-log10 adjusted p-value", color = "Regulation")
}
# Example of function usage
plotVolcano(r, paste(groups[1], "vs", groups[3]))## Warning: Removed 13 rows containing missing values or values outside the scale range
## (`geom_point()`).## Warning: Removed 422 rows containing missing values or values outside the scale range
## (`geom_text_repel()`).
# Genes upregulated
up_genes <- rownames(subset(r, padj < 0.05 & log2FoldChange >= 1))
# Genes downregulated
down_genes <- rownames(subset(r, padj < 0.05 & log2FoldChange <= -1))
# All DEGs with |log2FC| > 2
de_genes <- c(up_genes, down_genes)
# Display gene symbols before conversion
expr_datasa <- as.data.frame(expr_data[rownames(expr_data) %in% de_genes, ])
# Convert expression data to long format for ggplot2
expr_datas <- as.data.frame(expr_datasa)
expr_datas$Gene <- rownames(expr_datas)
expr_datas <- pivot_longer(expr_datas, cols = -Gene, names_to = "Sample", values_to = "Expression")
expr_datas <- merge(expr_datas, pheno_data, by.x = "Sample", by.y = "geo_accession")
# Check column names and a sample of the data
expresse <- r[order(r$padj)[1:429], ]
expresse <- merge(as.data.frame(expresse), expr_datasa, by = 0, sort = F)
library(dplyr)
library(tibble)
library(clusterProfiler)
library(ggplot2)
r_df <- as.data.frame(r)
# This ensures that gene names are preserved
r_df_com_genes <- r_df %>%
rownames_to_column(var = "Gene")
# --- Now, the rest of your code works perfectly ---
top30_fc <- r_df_com_genes %>%
# O 'filter' também pode ser conflitante, é bom usar o prefixo
dplyr::filter(padj < 0.05 & abs(log2FoldChange) > 1) %>%
dplyr::arrange(desc(abs(log2FoldChange))) %>%
# Esta é a correção principal:
dplyr::slice(1:30) %>%
dplyr::mutate(
Regulation = case_when(
log2FoldChange > 1 ~ "Upregulated",
log2FoldChange < -1 ~ "Downregulated"
)
)
# Graph with positive and negative bars (your code here is perfect)
ggplot(top30_fc, aes(x = reorder(Gene, log2FoldChange), y = log2FoldChange, fill = Regulation)) +
geom_col() +
coord_flip() + # Coloca os genes no eixo Y
scale_fill_manual(values = c("Upregulated" = "steelblue", "Downregulated" = "tomato")) +
scale_y_continuous(breaks = seq(-8, 4, by = 1)) + # Ajuste os limites se necessário
theme_bw() +
labs(
title = "The 30 most prominent DEGs between PsA and Healthy (GSE117769)",
x = "Gene",
y = "log2 Fold Change",
fill = "Regulation"
) +
theme(
axis.text.y = element_text(color = "black", face = "bold", size = 9)
)
# --- Select the 20 MOST overexpressed genes ---
up_20genes <- expresse %>%
filter(padj < 0.05 & log2FoldChange > 1) %>%
arrange(desc(log2FoldChange)) %>%
head(20) %>%
pull(Row.names)
# --- Filters expression data ---
expr_datas_filtrado_up <- expr_datas %>%
filter(`characteristics_ch1.6` %in% c("phenotype: Psoriatic arthritis", "phenotype: Healthy")) %>%
filter(Gene %in% up_20genes)
# --- Calculate the average per gene and per group ---
expr_datasa_up <- expr_datas_filtrado_up %>%
group_by(Gene, `characteristics_ch1.6`) %>%
summarise(
mean_expression = mean(Expression, na.rm = TRUE),
sd_expression = sd(Expression, na.rm = TRUE),
.groups = 'drop'
)
# --- Preparation for the chart ---
dados_para_plotar_up <- expr_datasa_up %>%
filter(characteristics_ch1.6 == "phenotype: Psoriatic arthritis")
# --- Graph Generation ---
ggplot(dados_para_plotar_up, aes(x = mean_expression, y = reorder(Gene, mean_expression))) +
geom_col(fill = "steelblue", color = "black", width = 0.7) +
labs(
title = "Average Expression of the Main Upregulated Genes in Psoriatic arthritis", # Título mais claro
subtitle = "For PsA vs Healthy (GSE117769)",
x = "Average Expression in the Group 'PsA'", # Rótulo do eixo mais claro
y = "Gene"
) +
theme_minimal(base_size = 14) +
theme(
panel.grid.major.y = element_blank(),
axis.text.y = element_text(size = 12)
)
# --- Selects the 20 MOST under-expressed genes ---
down_20genes <- expresse %>%
filter(padj < 0.05 & log2FoldChange < -1) %>%
arrange(log2FoldChange) %>% # <-- Sort from most negative to least negative
head(20) %>%
pull(Row.names)
# --- Filters expression data for genes and groups of interest ---
expr_datas_filtrado_down <- expr_datas %>%
filter(`characteristics_ch1.6` %in% c("phenotype: Psoriatic arthritis", "phenotype: Healthy")) %>%
filter(Gene %in% down_20genes)
# --- Calculate the average per gene and per group ---
expr_datasa_down <- expr_datas_filtrado_down %>%
group_by(Gene, `characteristics_ch1.6`) %>%
summarise(
mean_expression = mean(Expression, na.rm = TRUE),
.groups = 'drop'
)
# --- Preparation for the chart ---'
dados_para_plotar <- expr_datasa_down %>%
filter(characteristics_ch1.6 == "phenotype: Psoriatic arthritis")
# --- Graph Generation ---
ggplot(dados_para_plotar, aes(x = mean_expression, y = reorder(Gene, -mean_expression))) +
geom_col(fill = "red", color = "black", width = 0.7) +
labs(
title = "Average Expression of the Main Downregulated Genes in Psoriatic arthritis", # Título mais claro
subtitle = "For PsA vs Healthy (GSE117769)",
x = "Average Expression in the Group 'PsA'", # Rótulo do eixo mais claro
y = "Gene"
) +
theme_minimal(base_size = 14) +
theme(
panel.grid.major.y = element_blank(),
axis.text.y = element_text(size = 12)
)
# --- Create 'count_matrix' ---
up_genes <- rownames(subset(r, padj < 0.05 & log2FoldChange > 1))
down_genes <- rownames(subset(r, padj < 0.05 & log2FoldChange < -1))
genes_interesse <- c(up_genes, down_genes)
expr_filtrado <- expr_datas %>%
filter(`characteristics_ch1.6` %in% c("phenotype: Psoriatic arthritis", "phenotype: Healthy")) %>%
filter(Gene %in% genes_interesse)
matriz_contagem <- expr_filtrado %>%
select(Gene, Sample, Expression) %>%
pivot_wider(names_from = Sample, values_from = Expression, values_fill = 0) %>%
column_to_rownames(var = "Gene")
# Filter your original “sample_info” object to keep only the samples that are in your final matrix.
# This ensures that the annotation corresponds exactly to the heatmap data.
sample_info_filtrado <- subset(sample_info, rownames(sample_info) %in% colnames(matriz_contagem))
# Select the 20 most highly expressed genes
media_dos_genes <- rowMeans(matriz_contagem)
media_ordenada <- sort(media_dos_genes, decreasing = TRUE)
top_20_genes_por_media <- names(head(media_ordenada, 20))
heatmapData_top20 <- as.matrix(matriz_contagem[top_20_genes_por_media, ])
# Create the annotation for the heatmap from the already filtered information.
annotation_data <- data.frame(
Group = sample_info_filtrado$Group,
row.names = rownames(sample_info_filtrado)
)
# Ensure that the order of the columns in the heatmap and annotation is the same.
heatmapData_top20 <- heatmapData_top20[, rownames(annotation_data)]
# --- Heatmap generation with ComplexHeatmap ---
library(ComplexHeatmap)
library(circlize)
library(RColorBrewer)
# Rescale data by row (Z-score)
mat_scaled <- t(scale(t(heatmapData_top20)))
# Create the column annotation
ha_col <- HeatmapAnnotation(
Group = annotation_data$Group,
col = list(Group = c("PsA" = "red", "Healthy" = "yellow"))
)
# Define the colour palette
cores <- colorRamp2(c(-2, 0, 2), rev(RColorBrewer::brewer.pal(3, "RdBu")))
# Generate the heatmap
Heatmap(
mat_scaled,
name = "Z-score",
top_annotation = ha_col,
col = cores,
# Divide the columns into groups for clearer viewing
column_split = annotation_data$Group,
cluster_rows = TRUE,
cluster_columns = TRUE, # Cluster within each divided group
show_column_names = FALSE,
show_row_names = TRUE,
column_title = "Heatmap of the most highly expressed DEGs (PsA vs. Healthy GSE117769)",
heatmap_legend_param = list(title = "Z-score")
)
# Filter differentially expressed genes
de_genes <- subset(r, padj < 0.05 & abs(log2FoldChange) > 1)
# Create a data frame from de_genes
de_genes <- data.frame(de_genes)
# Suppose your dataframe is called df and you want to select columns ‘column1’, “column2” and ‘column3’.
de_genes <- de_genes %>% select(log2FoldChange, padj)
# Assuming that rownames(df) are gene symbols
gene_symbols <- rownames(de_genes)
# Convert gene symbols to Entrez IDs
gene_entrez_ids <- bitr(gene_symbols, fromType = "SYMBOL", toType = "ENTREZID", OrgDb = org.Hs.eg.db)## 'select()' returned 1:1 mapping between keys and columns# First, convert the rownames from df into a column
de_genes$Symbol <- rownames(de_genes)
# Join the original table and the converted IDs
de_genes <- merge(de_genes, gene_entrez_ids, by.x = "Symbol", by.y = "SYMBOL", all.x = TRUE)
# Ensure unique symbols
de_genes <- de_genes[!duplicated(de_genes$ENTREZID), ]
# View the first results to verify the addition of the IDs
de_genes <- de_genes %>%
filter(Symbol %in% rownames(matriz_contagem))
BiocManager::install("GOSemSim")## 'getOption("repos")' replaces Bioconductor standard repositories, see
## 'help("repositories", package = "BiocManager")' for details.
## Replacement repositories:
## CRAN: https://p3m.dev/cran/__linux__/jammy/latest## Bioconductor version 3.20 (BiocManager 1.30.26), R 4.4.1 (2024-06-14)## Installing package(s) 'GOSemSim'## Warning in install.packages(...): installation of package 'GOSemSim' had
## non-zero exit status## Installation paths not writeable, unable to update packages
## path: /usr/local/lib/R/library
## packages:
## boot, class, cluster, foreign, KernSmooth, lattice, MASS, Matrix, mgcv,
## nlme, nnet, rpart, spatial, survival
## path: /usr/local/lib/R/site-library
## packages:
## annotate, AnnotationDbi, ape, aplot, askpass, BH, Biobase, BiocFileCache,
## BiocGenerics, BiocManager, BiocParallel, BiocVersion, biomaRt, Biostrings,
## bit, bit64, bitops, Boruta, broom, bslib, C50, car, caret, checkmate, chk,
## classInt, cli, clock, clue, clusterProfiler, colorspace, commonmark,
## ComplexHeatmap, corrplot, cowplot, cpp11, credentials, crosstalk, Cubist,
## cutpointr, dbplyr, dbscan, DelayedArray, DEoptimR, Deriv, DESeq2, devtools,
## DiceKriging, diffobj, doBy, docopt, DOSE, dotCall64, downloader, DT,
## dtplyr, edgeR, enrichplot, entropy, evaluate, fastDummies, fastmatch,
## fgsea, fitdistrplus, fontawesome, forcats, fs, future, future.apply,
## gargle, GDCRNATools, genefilter, generics, GenomeInfoDb, GenomeInfoDbData,
## GenomicDataCommons, GenomicRanges, gert, ggforce, ggfun, ggnewscale,
## ggplot2, ggplotify, ggpubr, ggraph, ggridges, ggsci, ggtree, gh, gld,
## glmnet, globals, glue, GO.db, googledrive, googlesheets4, GOSemSim, gower,
## GPArotation, gplots, graph, graphlayouts, gtable, hardhat, haven, HDO.db,
## here, hms, httpuv, httr2, IRanges, jpeg, jsonlite, KEGGgraph, KEGGREST,
## keras, KMsurv, knitr, labelled, later, lava, lavaan, lgr, limma, littler,
## lme4, lmom, locfit, lubridate, magrittr, markdown, MatchIt, MatrixGenerics,
## MatrixModels, matrixStats, maxstat, mice, mime, miniUI, mlbench, mlr3,
## mlr3learners, mlr3measures, mlr3misc, mlr3pipelines, modeltools, multcomp,
## mvtnorm, networkD3, nloptr, org.Hs.eg.db, party, partykit, patchwork,
## pathview, pbapply, pbkrtest, pillar, pkgbuild, pkgdown, pkgload, plotly,
## pROC, processx, prodlim, progressr, PRROC, ps, psych, purrr, quantmod,
## quantreg, questionr, qvalue, R.cache, R.oo, R.utils, R6, ragg, ranger,
## Rcpp, RcppArmadillo, RcppTOML, RCurl, readxl, recipes, reshape, rgl,
## Rgraphviz, rlang, rmarkdown, robustbase, roxygen2, rprojroot, rsq, rstatix,
## rstudioapi, rversions, rvest, S4Arrays, S4Vectors, sass, scales,
## scatterpie, sctransform, sessioninfo, Seurat, SeuratObject, shadowtext,
## shiny, sp, spam, SparseArray, spatstat.data, spatstat.explore,
## spatstat.geom, spatstat.random, spatstat.univar, spatstat.utils, statmod,
## stringi, stringr, styler, SummarizedExperiment, survminer, sva, svglite,
## sys, systemfonts, TCGAbiolinks, TCGAbiolinksGUI.data, tensor, tensorflow,
## testthat, textshaping, tfruns, TH.data, tibble, timeDate, tinytex, treeio,
## tzdb, UCSC.utils, usethis, utf8, uwot, VIM, vroom, waldo, withr, xgboost,
## XML, xml2, xts, XVector, yulab.utils, zeallot, zip, zlibbioc, zoo## Old packages: 'curl', 'data.table', 'Hmisc', 'igraph', 'openssl', 'parallelly',
## 'promises', 'reticulate', 'RSQLite', 'xfun'library(GOSemSim)
BiocManager::install("enrichplot")## 'getOption("repos")' replaces Bioconductor standard repositories, see
## 'help("repositories", package = "BiocManager")' for details.
## Replacement repositories:
## CRAN: https://p3m.dev/cran/__linux__/jammy/latest## Bioconductor version 3.20 (BiocManager 1.30.26), R 4.4.1 (2024-06-14)## Installing package(s) 'enrichplot'## also installing the dependencies 'DOSE', 'GOSemSim'## Warning in install.packages(...): installation of package 'GOSemSim' had
## non-zero exit status## Warning in install.packages(...): installation of package 'DOSE' had non-zero
## exit status## Warning in install.packages(...): installation of package 'enrichplot' had
## non-zero exit status## Installation paths not writeable, unable to update packages
## path: /usr/local/lib/R/library
## packages:
## boot, class, cluster, foreign, KernSmooth, lattice, MASS, Matrix, mgcv,
## nlme, nnet, rpart, spatial, survival
## path: /usr/local/lib/R/site-library
## packages:
## annotate, AnnotationDbi, ape, aplot, askpass, BH, Biobase, BiocFileCache,
## BiocGenerics, BiocManager, BiocParallel, BiocVersion, biomaRt, Biostrings,
## bit, bit64, bitops, Boruta, broom, bslib, C50, car, caret, checkmate, chk,
## classInt, cli, clock, clue, clusterProfiler, colorspace, commonmark,
## ComplexHeatmap, corrplot, cowplot, cpp11, credentials, crosstalk, Cubist,
## cutpointr, dbplyr, dbscan, DelayedArray, DEoptimR, Deriv, DESeq2, devtools,
## DiceKriging, diffobj, doBy, docopt, DOSE, dotCall64, downloader, DT,
## dtplyr, edgeR, enrichplot, entropy, evaluate, fastDummies, fastmatch,
## fgsea, fitdistrplus, fontawesome, forcats, fs, future, future.apply,
## gargle, GDCRNATools, genefilter, generics, GenomeInfoDb, GenomeInfoDbData,
## GenomicDataCommons, GenomicRanges, gert, ggforce, ggfun, ggnewscale,
## ggplot2, ggplotify, ggpubr, ggraph, ggridges, ggsci, ggtree, gh, gld,
## glmnet, globals, glue, GO.db, googledrive, googlesheets4, GOSemSim, gower,
## GPArotation, gplots, graph, graphlayouts, gtable, hardhat, haven, HDO.db,
## here, hms, httpuv, httr2, IRanges, jpeg, jsonlite, KEGGgraph, KEGGREST,
## keras, KMsurv, knitr, labelled, later, lava, lavaan, lgr, limma, littler,
## lme4, lmom, locfit, lubridate, magrittr, markdown, MatchIt, MatrixGenerics,
## MatrixModels, matrixStats, maxstat, mice, mime, miniUI, mlbench, mlr3,
## mlr3learners, mlr3measures, mlr3misc, mlr3pipelines, modeltools, multcomp,
## mvtnorm, networkD3, nloptr, org.Hs.eg.db, party, partykit, patchwork,
## pathview, pbapply, pbkrtest, pillar, pkgbuild, pkgdown, pkgload, plotly,
## pROC, processx, prodlim, progressr, PRROC, ps, psych, purrr, quantmod,
## quantreg, questionr, qvalue, R.cache, R.oo, R.utils, R6, ragg, ranger,
## Rcpp, RcppArmadillo, RcppTOML, RCurl, readxl, recipes, reshape, rgl,
## Rgraphviz, rlang, rmarkdown, robustbase, roxygen2, rprojroot, rsq, rstatix,
## rstudioapi, rversions, rvest, S4Arrays, S4Vectors, sass, scales,
## scatterpie, sctransform, sessioninfo, Seurat, SeuratObject, shadowtext,
## shiny, sp, spam, SparseArray, spatstat.data, spatstat.explore,
## spatstat.geom, spatstat.random, spatstat.univar, spatstat.utils, statmod,
## stringi, stringr, styler, SummarizedExperiment, survminer, sva, svglite,
## sys, systemfonts, TCGAbiolinks, TCGAbiolinksGUI.data, tensor, tensorflow,
## testthat, textshaping, tfruns, TH.data, tibble, timeDate, tinytex, treeio,
## tzdb, UCSC.utils, usethis, utf8, uwot, VIM, vroom, waldo, withr, xgboost,
## XML, xml2, xts, XVector, yulab.utils, zeallot, zip, zlibbioc, zoo## Old packages: 'curl', 'data.table', 'Hmisc', 'igraph', 'openssl', 'parallelly',
## 'promises', 'reticulate', 'RSQLite', 'xfun'library(enrichplot)
BiocManager::install("STRINGdb")## 'getOption("repos")' replaces Bioconductor standard repositories, see
## 'help("repositories", package = "BiocManager")' for details.
## Replacement repositories:
## CRAN: https://p3m.dev/cran/__linux__/jammy/latest## Bioconductor version 3.20 (BiocManager 1.30.26), R 4.4.1 (2024-06-14)## Warning: package(s) not installed when version(s) same as or greater than current; use
## `force = TRUE` to re-install: 'STRINGdb'## Installation paths not writeable, unable to update packages
## path: /usr/local/lib/R/library
## packages:
## boot, class, cluster, foreign, KernSmooth, lattice, MASS, Matrix, mgcv,
## nlme, nnet, rpart, spatial, survival
## path: /usr/local/lib/R/site-library
## packages:
## annotate, AnnotationDbi, ape, aplot, askpass, BH, Biobase, BiocFileCache,
## BiocGenerics, BiocManager, BiocParallel, BiocVersion, biomaRt, Biostrings,
## bit, bit64, bitops, Boruta, broom, bslib, C50, car, caret, checkmate, chk,
## classInt, cli, clock, clue, clusterProfiler, colorspace, commonmark,
## ComplexHeatmap, corrplot, cowplot, cpp11, credentials, crosstalk, Cubist,
## cutpointr, dbplyr, dbscan, DelayedArray, DEoptimR, Deriv, DESeq2, devtools,
## DiceKriging, diffobj, doBy, docopt, DOSE, dotCall64, downloader, DT,
## dtplyr, edgeR, enrichplot, entropy, evaluate, fastDummies, fastmatch,
## fgsea, fitdistrplus, fontawesome, forcats, fs, future, future.apply,
## gargle, GDCRNATools, genefilter, generics, GenomeInfoDb, GenomeInfoDbData,
## GenomicDataCommons, GenomicRanges, gert, ggforce, ggfun, ggnewscale,
## ggplot2, ggplotify, ggpubr, ggraph, ggridges, ggsci, ggtree, gh, gld,
## glmnet, globals, glue, GO.db, googledrive, googlesheets4, GOSemSim, gower,
## GPArotation, gplots, graph, graphlayouts, gtable, hardhat, haven, HDO.db,
## here, hms, httpuv, httr2, IRanges, jpeg, jsonlite, KEGGgraph, KEGGREST,
## keras, KMsurv, knitr, labelled, later, lava, lavaan, lgr, limma, littler,
## lme4, lmom, locfit, lubridate, magrittr, markdown, MatchIt, MatrixGenerics,
## MatrixModels, matrixStats, maxstat, mice, mime, miniUI, mlbench, mlr3,
## mlr3learners, mlr3measures, mlr3misc, mlr3pipelines, modeltools, multcomp,
## mvtnorm, networkD3, nloptr, org.Hs.eg.db, party, partykit, patchwork,
## pathview, pbapply, pbkrtest, pillar, pkgbuild, pkgdown, pkgload, plotly,
## pROC, processx, prodlim, progressr, PRROC, ps, psych, purrr, quantmod,
## quantreg, questionr, qvalue, R.cache, R.oo, R.utils, R6, ragg, ranger,
## Rcpp, RcppArmadillo, RcppTOML, RCurl, readxl, recipes, reshape, rgl,
## Rgraphviz, rlang, rmarkdown, robustbase, roxygen2, rprojroot, rsq, rstatix,
## rstudioapi, rversions, rvest, S4Arrays, S4Vectors, sass, scales,
## scatterpie, sctransform, sessioninfo, Seurat, SeuratObject, shadowtext,
## shiny, sp, spam, SparseArray, spatstat.data, spatstat.explore,
## spatstat.geom, spatstat.random, spatstat.univar, spatstat.utils, statmod,
## stringi, stringr, styler, SummarizedExperiment, survminer, sva, svglite,
## sys, systemfonts, TCGAbiolinks, TCGAbiolinksGUI.data, tensor, tensorflow,
## testthat, textshaping, tfruns, TH.data, tibble, timeDate, tinytex, treeio,
## tzdb, UCSC.utils, usethis, utf8, uwot, VIM, vroom, waldo, withr, xgboost,
## XML, xml2, xts, XVector, yulab.utils, zeallot, zip, zlibbioc, zoo## Old packages: 'curl', 'data.table', 'Hmisc', 'igraph', 'openssl', 'parallelly',
## 'promises', 'reticulate', 'RSQLite', 'xfun'library(STRINGdb)
#Alternative Workflow with STRINGdb Integration in R
# Initialise the STRINGdb object for a specific organism
string_db <- STRINGdb$new(version = "12", species = 9606, score_threshold = 400, input_directory = "")
options(timeout = 600) # increases to 10 minutes
# Gene mapping using STRINGdb
mapped_genes <- string_db$map(de_genes, "Symbol", removeUnmappedRows = TRUE)
# Recover interactions for mapped genes
interactions <- string_db$get_interactions(mapped_genes$STRING_id)
# Visualise the network using igraph or other visualisation tools
library(igraph)##
## Attaching package: 'igraph'## The following object is masked from 'package:tibble':
##
## as_data_frame## The following objects are masked from 'package:rtracklayer':
##
## blocks, path## The following object is masked from 'package:BiocIO':
##
## path## The following object is masked from 'package:Biostrings':
##
## union## The following object is masked from 'package:XVector':
##
## path## The following object is masked from 'package:circlize':
##
## degree## The following objects are masked from 'package:topGO':
##
## algorithm, graph## The following objects are masked from 'package:graph':
##
## degree, edges, intersection, union## The following object is masked from 'package:clusterProfiler':
##
## simplify## The following object is masked from 'package:tidyr':
##
## crossing## The following objects are masked from 'package:dplyr':
##
## as_data_frame, groups, union## The following object is masked from 'package:GenomicRanges':
##
## union## The following object is masked from 'package:IRanges':
##
## union## The following object is masked from 'package:S4Vectors':
##
## union## The following objects are masked from 'package:BiocGenerics':
##
## normalize, path, union## The following objects are masked from 'package:stats':
##
## decompose, spectrum## The following object is masked from 'package:base':
##
## uniong <- graph_from_data_frame(interactions, directed=FALSE)
plot(g)
# Detect clusters (e.g. Louvain)
clusters <- cluster_louvain(g)
# Plot with colours by cluster
plot(g, vertex.color=clusters$membership)
# Perform GO enrichment analysis
# Biological Process
# Ensure you have the packages installed
library(clusterProfiler)
library(org.Hs.eg.db)
library(ggplot2)
library(dplyr) # For data manipulation
# Biological Process
enrich_result <- enrichGO(gene = mapped_genes$Symbol,
OrgDb = org.Hs.eg.db,
keyType = "SYMBOL",
ont = "BP", # Biological Ontology. It can be ‘BP’, “MF”, or ‘CC’
pAdjustMethod = "BH", # Benjamini-Hochberg (BH) is the same as FDR.
pvalueCutoff = 0.05,
qvalueCutoff = 0.2)
if (is.null(enrich_result) || nrow(as.data.frame(enrich_result)) == 0) {
print("No significantly enriched GO terms were found with the provided criteria.")
} else {
plot_data <- as.data.frame(enrich_result) %>%
arrange(p.adjust) %>%
head(15) # Display the 15 most significant terms
# Create a numeric column for the Y axis to use with geom_segment
# The order of the terms on the Y axis is important.
plot_data$y_pos <- rev(seq_along(plot_data$Description)) # To sort from top to bottom
ggplot(plot_data, aes(x = Count, y = y_pos)) + # Use y_pos for the Y axis
# Add geom_segment for the ‘threads’
# It starts at x=0 (or a small value) and goes up to the Count of the term.
geom_segment(aes(x = 0, xend = Count, y = y_pos, yend = y_pos),
color = "gray", linewidth = 0.5) +
geom_point(aes(size = Count, color = p.adjust), alpha = 0.8) +
scale_color_gradientn(
colors = c("darkblue", "steelblue", "lightblue", "lightgreen", "yellow", "orange", "darkred"),
name = "FDR",
trans = "log10",
breaks = scales::trans_breaks("log10", function(x) 10^x),
labels = scales::trans_format("log10", scales::math_format(10^.x))
) +
scale_size_area(max_size = 15, name = "Contagem de Genes") +
# Map labels back to GO descriptions
scale_y_continuous(breaks = plot_data$y_pos, labels = plot_data$Description) +
labs(
title = "GO Enrichment Analysis (Biological Processes)",
x = "Genes Counting",
y = "GO Terms (Biological Processes)"
) +
theme_minimal() +
theme(
axis.text.y = element_text(size = 12, face = "bold"),
axis.title = element_text(size = 14, face = "bold"),
plot.title = element_text(size = 16, face = "bold", hjust = 0.5),
legend.position = "right",
legend.title = element_text(size = 12, face = "bold"),
legend.text = element_text(size = 10),
panel.grid.major.y = element_blank(), # Remove the default horizontal grid lines
panel.grid.minor = element_blank(),
panel.border = element_rect(colour = "black", fill=NA, linewidth=1)
)
}
barplot(enrich_result, showCategory = 10, title= "GO Enrichment Analysis")## Warning in fortify(object, showCategory = showCategory, by = x, ...): Arguments in `...` must be used.
## ✖ Problematic argument:
## • by = x
## ℹ Did you misspell an argument name?## Warning: `aes_string()` was deprecated in ggplot2 3.0.0.
## ℹ Please use tidy evaluation idioms with `aes()`.
## ℹ See also `vignette("ggplot2-in-packages")` for more information.
## ℹ The deprecated feature was likely used in the enrichplot package.
## Please report the issue at
## <https://github.com/GuangchuangYu/enrichplot/issues>.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.
# Network graph of enriched terms
cnetplot(enrich_result, showCategory = 10)## Warning: `aes_()` was deprecated in ggplot2 3.0.0.
## ℹ Please use tidy evaluation idioms with `aes()`
## ℹ The deprecated feature was likely used in the enrichplot package.
## Please report the issue at
## <https://github.com/GuangchuangYu/enrichplot/issues>.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.
# Heatmap
heatplot(enrich_result, showCategory = 10)
# Perform KEGG enrichment analysis
ekegg <- enrichKEGG(gene = mapped_genes$ENTREZID, organism = "hsa", pAdjustMethod = "BH", qvalueCutoff = 0.05)## Reading KEGG annotation online: "https://rest.kegg.jp/link/hsa/pathway"...## Reading KEGG annotation online: "https://rest.kegg.jp/list/pathway/hsa"...# Generate GO/STRING style bubble chart
if (is.null(ekegg) || nrow(as.data.frame(ekegg)) == 0) {
print("No significantly enriched KEGG pathways were found with the criteria provided.")
} else {
plot_data_kegg <- as.data.frame(ekegg) %>%
arrange(p.adjust) %>% # Sort by p.adjust (FDR)
head(15) # Selects the 15 most significant pathways to plot
# Creates a numerical position for the terms on the Y-axis, to control the order and lines
plot_data_kegg$y_pos <- rev(seq_along(plot_data_kegg$Description)) # reverse to the most significant at the top
# Starting to build the graph with ggplot2
ggplot(plot_data_kegg, aes(x = Count, y = y_pos)) +
# Adds the connection lines (wires) from the Y-axis to the bubble.
geom_segment(aes(x = 0, xend = Count, y = y_pos, yend = y_pos),
color = "gray80", linewidth = 0.6) + # Softer colour for the lines
# Add the bubbles
geom_point(aes(size = Count, color = p.adjust), alpha = 0.9) +
# Colour scale configuration for FDR (p.adjust)
scale_color_gradientn(
colors = c("darkblue", "steelblue", "lightblue", "lightgreen", "yellow", "orange", "darkred"),
name = "FDR",
trans = "log10", # Use logarithmic scale for FDR
breaks = scales::trans_breaks("log10", function(x) 10^x), # Breaks in scientific notation captions
labels = scales::trans_format("log10", scales::math_format(10^.x)), # Scientific notation format
limits = c(min(plot_data_kegg$p.adjust), max(plot_data_kegg$p.adjust)) # Sets limits for data
) +
# Size scale configuration for Gene Counting
scale_size_area(
max_size = 18, # Maximum bubble size
name = "Gene count", # Caption title size
breaks = unique(round(quantile(plot_data_kegg$Count, probs = c(0.25, 0.5, 0.75, 1.0)))), # Suggests reasonable breaks
labels = unique(round(quantile(plot_data_kegg$Count, probs = c(0.25, 0.5, 0.75, 1.0))))
) +
# Maps the Y-axis labels back to the KEGG pathway descriptions
scale_y_continuous(
breaks = plot_data_kegg$y_pos,
labels = plot_data_kegg$Description
) +
# Labels and Chart Title
labs(
title = "KEGG Pathway Enrichment Analysis",
x = "Gene count", # X-axis is now Gene Count
y = "KEGG Pathway" # Y-axis is the name of the pathway
) +
# Chart Theme and Style
theme_minimal() +
theme(
axis.text.y = element_text(size = 12, face = "bold"), # KEGG terms in bold and larger font
axis.title = element_text(size = 14, face = "bold"), # Axis titles
plot.title = element_text(size = 16, face = "bold", hjust = 0.5), # Centred title
legend.position = "right", # Position of subtitles
legend.title = element_text(size = 12, face = "bold"),
legend.text = element_text(size = 10),
panel.grid.major.y = element_blank(), # Remove standard horizontal grid lines
panel.grid.minor = element_blank(), # Remove minor grid liness
panel.border = element_rect(colour = "black", fill=NA, linewidth=1.2) # Black border around the plot
)
} 
barplot(ekegg, showCategory = 10, title = "KEGG Enrichment Analysis")## Warning in fortify(object, showCategory = showCategory, by = x, ...): Arguments in `...` must be used.
## ✖ Problematic argument:
## • by = x
## ℹ Did you misspell an argument name?
# Network graph of enriched terms
cnetplot(ekegg, showCategory = 10)
# Heatmap
heatplot(ekegg, showCategory = 10)
7.Transcription factors in the analysis between PsA vs Healthy
# Load the necessary packages
library(GenomicFeatures)##
## Attaching package: 'GenomicFeatures'## The following object is masked from 'package:topGO':
##
## geneslibrary(TxDb.Hsapiens.UCSC.hg38.knownGene)
library(org.Hs.eg.db)
library(JASPAR2020)
library(TFBSTools)
library(SummarizedExperiment)
library(motifmatchr)
# Load the TxDb database
txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene
# Extraction of exons by gene
exons_by_gene <- exonsBy(txdb, by = "gene")
# Obtain the coordinates of the genes (taking the first and last positions of the exons)
genes_info <- range(exons_by_gene)
# Obtain transcription information
transcripts_info <- transcripts(txdb)
# Map genes of interest to Entrez IDs (replace “de_genes” with the actual list of genes)
gene_entrez <- mapIds(org.Hs.eg.db, keys = mapped_genes$Symbol, column = "ENTREZID", keytype = "SYMBOL", multiVals = "first")## 'select()' returned 1:1 mapping between keys and columns# Filter the genes of interest
promoters_info <- subset(genes_info, names(genes_info) %in% gene_entrez)
# Define promoter regions (2 kb upstream of TSS)
promoters <- promoters(promoters_info, upstream = 2000, downstream = 0)
# Filter the main chromosomes
promoters <- keepStandardChromosomes(promoters, pruning.mode = "coarse")
# Remove any regions that exceed the limits of the chromosomes.
promoters <- trim(promoters)
# Convert CompressedGRangesList promoters to GRanges
promoters_gr <- unlist(promoters)
# Load the JASPAR grounds database
motifs <- getMatrixSet(JASPAR2020, opts = list(species = "Homo sapiens"))
# Create a data frame with the IDs of the reasons and their names (TFs)
motif_info <- data.frame(
motif_id = names(motifs),
tf_name = sapply(motifs, function(x) x@name),
stringsAsFactors = FALSE
)
# Enriching motifs in promoting regions
motifHits <- matchMotifs(motifs, promoters_gr, genome = BSgenome.Hsapiens.UCSC.hg38)
# Count the number of occurrences of the reasons in each promoting region.
motif_counts <- countOverlaps(promoters_gr, motifHits)
# Add counts to GRanges with promoting regions
promoters_gr$motif_counts <- motif_counts
# Summary of motif counts
summary(promoters_gr$motif_counts)## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 0.0 0.0 0.5 0.5 1.0 1.0# Obtain the names of the motifs and TFs
motif_names <- names(motifHits)
# Extract the reason table from the RangedSummarizedExperiment object
motif_data <- assays(motifHits)[[1]] # Assuming that the table of reasons is in the first list of assays
# Obtain information about TFs
# The names of TFs may be in the colnames or in associated metadata
tf_names <- colnames(motif_data)
# Add the reason count if available
motif_counts <- rowSums(motif_data)
# Check the dimensions of the motif_data object
dim(motif_data) # Number of rows and columns## [1] 6 633# Check the length of tf_names and motif_counts
tf_names_length <- length(tf_names)
motif_counts_length <- length(motif_counts)
# Print the lengths for diagnosis
cat("Length of tf_names:", tf_names_length, "\n")## Length of tf_names: 633cat("Length of motif_counts:", motif_counts_length, "\n")## Length of motif_counts: 6# Verify that the dimensions of motif_data correspond to the number of TFs and motifs
motif_data_dims <- dim(motif_data)
cat("Dimensions of motif_data (rows, columns):", motif_data_dims, "\n")## Dimensions of motif_data (rows, columns): 6 633# Check whether the number of reasons is greater or lesser
if (tf_names_length > motif_counts_length) {
# Check additional columns
tf_names <- tf_names[1:motif_counts_length] # Adjust to the length of motif_counts
} else {
# Adjust motif_counts to match tf_names
motif_counts <- motif_counts[1:tf_names_length]
}
# Now, create the data frame with adjusted lengths
motif_summary <- data.frame(
tf_name = tf_names,
motif_count = motif_counts
)
# Check the correspondence between TF names and the columns in motif_data
all(tf_names %in% colnames(motif_data)) # Should return TRUE if all TF names are present## [1] TRUE# Sort and identify key TFs
tf_summary <- motif_summary[order(motif_summary$motif_count, decreasing = TRUE), ]
top_tf_summary <- head(tf_summary, 121) # Adjust the number as required
# Mapping Entrez IDs to gene symbols
gene_symbols <- mapIds(org.Hs.eg.db, keys = rownames(top_tf_summary), column = "SYMBOL", keytype = "ENTREZID", multiVals = "first")## 'select()' returned 1:1 mapping between keys and columns# Replace rownames with gene symbols
rownames(top_tf_summary) <- gene_symbols
# Add reason ID as a column
top_tf_summary$motif_id <- rownames(top_tf_summary)
# Add to the table of TF names
motif1 <- merge(top_tf_summary, motif_info, by.x = "tf_name", by.y = "motif_id")
# Reorder columns
motif2 <- motif1[, c("motif_id", "tf_name.y", "motif_count")]
colnames(motif2) <- c("motif_id", "tf_name", "motif_count")
# Sort by frequency (motif_count) in descending order
motif2 <- motif2 %>% arrange(desc(motif_count))
print(motif2)## motif_id tf_name motif_count
## 1 TNFAIP3 MAX::MYC 190
## 2 IL6 IRF2 148
## 3 DUSP4 FOXF2 144
## 4 OLR1 MZF1(var.2) 144
## 5 CD69 PPARG 131
## 6 CLEC4D FOXD1 1118. Comparison between peripheral blood samples from AS patients and control samples.
# Wald test to obtain contrast-specific results
dsd <- DESeq(dsa, test = "Wald", sfType = "poscount")## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing## -- replacing outliers and refitting for 9 genes
## -- DESeq argument 'minReplicatesForReplace' = 7
## -- original counts are preserved in counts(dds)## estimating dispersions## fitting model and testingr <- results(dsd, contrast = c("Group", groups[2], groups[3]), alpha = 0.05, pAdjustMethod = "fdr")
groups <- levels(colData(dsd)$Group)
df <- as.data.frame(r)
# Filter only significant genes
sig_genes <- subset(r, padj < 0.05 & abs(log2FoldChange) >= 1)
# volcano plot
old.pal <- palette(c("#00BFFF", "#FF3030")) # low-hi colors
par(mar=c(4,4,2,1), cex.main=1.5)
with(sig_genes, {
plot(log2FoldChange, -log10(padj), main=paste(groups[2], "vs", groups[3]),
xlab="log2FC", ylab="-log10(Padj)", pch=20, cex=0.5)
text(log2FoldChange, -log10(padj), labels=rownames(r), cex=0.6, pos=4)
})
with(subset(r, padj<0.05 & abs(log2FoldChange) >= 1),
points(log2FoldChange, -log10(padj), pch=20, col=(sign(log2FoldChange) + 3)/2, cex=1))
legend("bottomleft", title=paste("Padj<", 0.05, sep=""), legend=c("down", "up"), pch=20,col=1:2)
# Plot only significant genes
# MD PLOT
par(mar=c(4,4,2,1), cex.main=1.5)
with(sig_genes, {
plot(log10(baseMean), log2FoldChange,
main=paste(groups[2], "vs", groups[3]),
xlab="log10(mean of normalized counts)", ylab="log2FoldChange",
pch=20, col=(sign(log2FoldChange) + 3)/2, cex=1)
text(log10(baseMean), log2FoldChange, labels=rownames(sig_genes), cex=0.6, pos=4)
})
legend("bottomleft", title=paste("Padj<", 0.05, sep=""), legend=c("down", "up"), pch=20, col=1:2)
abline(h=0)
palette(old.pal) # restore palette
# Add gene symbols to the points on the graph
# Install the packages if you do not already have them
library(ggplot2)
library(ggrepel)
plotVolcano <- function(res, title = "Volcano Plot") {
res$group <- "NS"
res$group[res$padj < 0.05 & res$log2FoldChange > 1] <- "Up"
res$group[res$padj < 0.05 & res$log2FoldChange < -1] <- "Down"
res$label <- ifelse(res$group != "NS", rownames(res), NA)
ggplot(res, aes(x = log2FoldChange, y = -log10(padj), color = group)) +
geom_point(alpha = 0.7, size = 2) +
geom_hline(yintercept = -log10(0.05), linetype = "dashed") +
geom_vline(xintercept = c(-1, 1), linetype = "dashed") +
scale_color_manual(values = c("Up" = "firebrick", "Down" = "dodgerblue", "NS" = "grey80")) +
ggrepel::geom_text_repel(aes(label = label), size = 3, max.overlaps = Inf) +
theme_minimal() +
labs(title = title, x = "log2 Fold Change", y = "-log10 adjusted p-value", color = "Regulation")
}
# Example of function usage
plotVolcano(r, paste(groups[2], "vs", groups[3]))## Warning: Removed 62 rows containing missing values or values outside the scale range
## (`geom_point()`).## Warning: Removed 409 rows containing missing values or values outside the scale range
## (`geom_text_repel()`).
# Genes upregulated
up_genes <- rownames(subset(r, padj < 0.05 & log2FoldChange >= 1))
# Genes downregulated
down_genes <- rownames(subset(r, padj < 0.05 & log2FoldChange <= -1))
# All DEGs with |log2FC| > 2
de_genes <- c(up_genes, down_genes)
expr_datasa <- as.data.frame(expr_data[rownames(expr_data) %in% de_genes, ])
# Convert expression data to long format for ggplot2
expr_datas <- as.data.frame(expr_datasa)
expr_datas$Gene <- rownames(expr_datas)
expr_datas <- pivot_longer(expr_datas, cols = -Gene, names_to = "Sample", values_to = "Expression")
expr_datas <- merge(expr_datas, pheno_data, by.x = "Sample", by.y = "geo_accession")
# Check column names and a sample of the data
expresse <- r[order(r$padj)[1:429], ]
expresse <- merge(as.data.frame(expresse), expr_datasa, by = 0, sort = F)
library(dplyr)
library(tibble)
library(clusterProfiler)
library(ggplot2)
r_df <- as.data.frame(r)
# Assuming that “r_df” is your data frame with the DESeq2 results
# This ensures that gene names are preserved.
r_df_com_genes <- r_df %>%
rownames_to_column(var = "Gene")
top30_fc <- r_df_com_genes %>%
dplyr::filter(padj < 0.05 & abs(log2FoldChange) > 1) %>%
dplyr::arrange(desc(abs(log2FoldChange))) %>%
dplyr::slice(1:30) %>%
dplyr::mutate(
Regulation = case_when(
log2FoldChange > 1 ~ "Upregulated",
log2FoldChange < -1 ~ "Downregulated"
)
)
# Chart with positive and negative bars
ggplot(top30_fc, aes(x = reorder(Gene, log2FoldChange), y = log2FoldChange, fill = Regulation)) +
geom_col() +
coord_flip() + # Place the genes on the Y axis
scale_fill_manual(values = c("Upregulated" = "steelblue", "Downregulated" = "tomato")) +
scale_y_continuous(breaks = seq(-8, 4, by = 1)) + # Adjust the limits if necessary.
theme_bw() +
labs(
title = "The most prominent DEGs between AS and Healthy (GSE117769)",
x = "Gene",
y = "log2 Fold Change",
fill = "Regulation"
) +
theme(
axis.text.y = element_text(color = "black", face = "bold", size = 9)
)
# --- Selects the 20 MOST overexpressed genes ---
up_20genes <- expresse %>%
filter(padj < 0.05 & log2FoldChange > 1) %>%
arrange(desc(log2FoldChange)) %>%
head(20) %>%
pull(Row.names)
# --- Filters expression data ---
expr_datas_filtrado_up <- expr_datas %>%
filter(`characteristics_ch1.6` %in% c("phenotype: Ankylosing spondylitis", "phenotype: Healthy")) %>%
filter(Gene %in% up_20genes)
# --- Calculates the average per gene and per group ---
expr_datasa_up <- expr_datas_filtrado_up %>%
group_by(Gene, `characteristics_ch1.6`) %>%
summarise(
mean_expression = mean(Expression, na.rm = TRUE),
sd_expression = sd(Expression, na.rm = TRUE),
.groups = 'drop'
)
# --- Preparation for the chart ---
# Filter to show the average expression ONLY in the “non-lesion” group
dados_para_plotar_up <- expr_datasa_up %>%
filter(characteristics_ch1.6 == "phenotype: Ankylosing spondylitis")
# --- Graph Generation ---
ggplot(dados_para_plotar_up, aes(x = mean_expression, y = reorder(Gene, mean_expression))) +
geom_col(fill = "steelblue", color = "black", width = 0.7) +
labs(
title = "Average Expression of the Main Upregulated Genes in Ankylosing spondylitis", # Título mais claro
subtitle = "For AS vs Healthy (GSE117769)",
x = "Average Expression in the Group 'AS'", # Rótulo do eixo mais claro
y = "Gene"
) +
theme_minimal(base_size = 14) +
theme(
panel.grid.major.y = element_blank(),
axis.text.y = element_text(size = 12)
)
# --- Selects the 20 MOST under-expressed genes ---
down_20genes <- expresse %>%
filter(padj < 0.05 & log2FoldChange < -1) %>%
arrange(log2FoldChange) %>% # <-- Sort from most negative to least negative
head(20) %>%
pull(Row.names)
# --- Filters expression data for genes and groups of interest ---
expr_datas_filtrado_down <- expr_datas %>%
filter(`characteristics_ch1.6` %in% c("phenotype: Ankylosing spondylitis", "phenotype: Healthy")) %>%
filter(Gene %in% down_20genes)
# --- Calculates the average per gene and per group ---
expr_datasa_down <- expr_datas_filtrado_down %>%
group_by(Gene, `characteristics_ch1.6`) %>%
summarise(
mean_expression = mean(Expression, na.rm = TRUE),
.groups = 'drop'
)
# --- Preparation for the chart ---
# Filter to show the average expression ONLY in the “lesion” group
dados_para_plotar <- expr_datasa_down %>%
filter(characteristics_ch1.6 == "phenotype: Ankylosing spondylitis")
# --- Graph Generation ---
ggplot(dados_para_plotar, aes(x = mean_expression, y = reorder(Gene, -mean_expression))) +
geom_col(fill = "red", color = "black", width = 0.7) +
labs(
title = "Average Expression of the Main Downregulated Genes in Ankylosing spondylitis", # Título mais claro
subtitle = "For AS vs Healthy (GSE117769)",
x = "Average Expression in the Group 'AS'", # Rótulo do eixo mais claro
y = "Gene"
) +
theme_minimal(base_size = 14) +
theme(
panel.grid.major.y = element_blank(),
axis.text.y = element_text(size = 12)
)
# --- The code to create 'count_array' ---
up_genes <- rownames(subset(r, padj < 0.05 & log2FoldChange > 1))
down_genes <- rownames(subset(r, padj < 0.05 & log2FoldChange < -1))
genes_interesse <- c(up_genes, down_genes)
expr_filtrado <- expr_datas %>%
filter(`characteristics_ch1.6` %in% c("phenotype: Ankylosing spondylitis", "phenotype: Healthy")) %>%
filter(Gene %in% genes_interesse)
matriz_contagem <- expr_filtrado %>%
select(Gene, Sample, Expression) %>%
pivot_wider(names_from = Sample, values_from = Expression, values_fill = 0) %>%
column_to_rownames(var = "Gene")
# Filter your original “sample_info” object to keep only the samples that are in your final matrix
# This ensures that the annotation corresponds exactly to the heatmap data
sample_info_filtrado <- subset(sample_info, rownames(sample_info) %in% colnames(matriz_contagem))
# Select the 20 most highly expressed genes
media_dos_genes <- rowMeans(matriz_contagem)
media_ordenada <- sort(media_dos_genes, decreasing = TRUE)
top_20_genes_por_media <- names(head(media_ordenada, 20))
heatmapData_top20 <- as.matrix(matriz_contagem[top_20_genes_por_media, ])
# Create the annotation for the heatmap from the filtered and corrected information
annotation_data <- data.frame(
Group = sample_info_filtrado$Group,
row.names = rownames(sample_info_filtrado)
)
# Ensure that the order of the columns in the heatmap and annotation is the same
heatmapData_top20 <- heatmapData_top20[, rownames(annotation_data)]
# --- Heatmap generation with ComplexHeatmap ---
# Rescale data by row (Z-score)
mat_scaled <- t(scale(t(heatmapData_top20)))
# Create the column annotation
ha_col <- HeatmapAnnotation(
Group = annotation_data$Group,
col = list(Group = c("AS" = "#1f77b4", "Healthy" = "yellow"))
)
# Define the colour palette
cores <- colorRamp2(c(-2, 0, 2), rev(RColorBrewer::brewer.pal(3, "RdBu")))
# Generate the heatmap
Heatmap(
mat_scaled,
name = "Z-score",
top_annotation = ha_col,
col = cores,
# Divide the columns into groups for clearer viewing
column_split = annotation_data$Group,
cluster_rows = TRUE,
cluster_columns = TRUE, # Cluster within each divided group
show_column_names = FALSE,
show_row_names = TRUE,
column_title = "Heatmap of the most highly expressed DEGs (AS vs. Healthy GSE117769)",
heatmap_legend_param = list(title = "Z-score")
)
# Filter differentially expressed genes
de_genes <- subset(r, padj < 0.05 & abs(log2FoldChange) > 1)
#Create a data frame from de_genes
de_genes <- data.frame(de_genes)
# Suppose your dataframe is called df and you want to select columns ‘column1’, “column2” and ‘column3’
de_genes <- de_genes %>% select(log2FoldChange, padj)
# Assuming that rownames(df) are gene symbols
gene_symbols <- rownames(de_genes)
# Convert gene symbols to Entrez IDs
gene_entrez_ids <- bitr(gene_symbols, fromType = "SYMBOL", toType = "ENTREZID", OrgDb = org.Hs.eg.db)## 'select()' returned 1:1 mapping between keys and columns# First, convert the rownames from df into a column
de_genes$Symbol <- rownames(de_genes)
# Performs the join between the original table and the converted IDs
de_genes <- merge(de_genes, gene_entrez_ids, by.x = "Symbol", by.y = "SYMBOL", all.x = TRUE)
# Ensure unique symbols
de_genes <- de_genes[!duplicated(de_genes$ENTREZID), ]
# Alternative Workflow with STRINGdb Integration in R
# Initialise the STRINGdb object for a specific organism
string_db <- STRINGdb$new(version = "12", species = 9606, score_threshold = 400, input_directory = "")
options(timeout = 600) # increases to 10 minutes
# Gene mapping using STRINGdb
mapped_genes <- string_db$map(de_genes, "Symbol", removeUnmappedRows = TRUE)
# Recover interactions for mapped genes
interactions <- string_db$get_interactions(mapped_genes$STRING_id)
# Visualise the network using igraph or other visualisation tools
library(igraph)
g <- graph_from_data_frame(interactions, directed=FALSE)
plot(g)
# Detect clusters (e.g. Louvain)
clusters <- cluster_louvain(g)
# Plot with colours by cluster
plot(g, vertex.color=clusters$membership)
# Perform GO enrichment analysis
# Biological Process
enrich_result <- enrichGO(gene = mapped_genes$Symbol,
OrgDb = org.Hs.eg.db,
keyType = "SYMBOL",
ont = "BP", # Biological Ontology. It can be ‘BP’, “MF”, or ‘CC’.
pAdjustMethod = "BH",
pvalueCutoff = 0.05,
qvalueCutoff = 0.2)
barplot(enrich_result, showCategory = 10, title= "GO Enrichment Analysis")## Warning in fortify(object, showCategory = showCategory, by = x, ...): Arguments in `...` must be used.
## ✖ Problematic argument:
## • by = x
## ℹ Did you misspell an argument name?
# Network graph of enriched terms
cnetplot(enrich_result, showCategory = 10)
# Heatmap
heatplot(enrich_result, showCategory = 10)
# Perform KEGG enrichment analysis
ekegg <- enrichKEGG(gene = mapped_genes$ENTREZID, organism = "hsa", pAdjustMethod = "BH", qvalueCutoff = 0.05)
# Generate GO/STRING style bubble chart
if (is.null(ekegg) || nrow(as.data.frame(ekegg)) == 0) {
print("No significantly enriched KEGG pathways were found with the criteria provided.")
} else {
plot_data_kegg <- as.data.frame(ekegg) %>%
arrange(p.adjust) %>% # Sort by p.adjust (FDR)
head(15) # Selects the 15 most significant pathways to plot
# Creates a numerical position for the terms on the Y-axis, to control the order and lines
plot_data_kegg$y_pos <- rev(seq_along(plot_data_kegg$Description)) # reverse to the most significant at the top
# Starting to build the graph with ggplot2
ggplot(plot_data_kegg, aes(x = Count, y = y_pos)) +
# Adds the connection lines (wires) from the Y-axis to the bubble
geom_segment(aes(x = 0, xend = Count, y = y_pos, yend = y_pos),
color = "gray80", linewidth = 0.6) + # Softer colour for the lines
# Add the bubbles
geom_point(aes(size = Count, color = p.adjust), alpha = 0.9) +
# Colour scale configuration for FDR (p.adjust)
scale_color_gradientn(
colors = c("darkblue", "steelblue", "lightblue", "lightgreen", "yellow", "orange", "darkred"),
name = "FDR",
trans = "log10", # Use logarithmic scale for FDR
breaks = scales::trans_breaks("log10", function(x) 10^x), # Breaks in scientific notation captions
labels = scales::trans_format("log10", scales::math_format(10^.x)), # Scientific notation format
limits = c(min(plot_data_kegg$p.adjust), max(plot_data_kegg$p.adjust)) # Sets limits for data
) +
# Size scale configuration for Gene Counting
scale_size_area(
max_size = 18, # Maximum bubble size
name = "Gene count", # Caption title size
breaks = unique(round(quantile(plot_data_kegg$Count, probs = c(0.25, 0.5, 0.75, 1.0)))), # Suggests reasonable breaks
labels = unique(round(quantile(plot_data_kegg$Count, probs = c(0.25, 0.5, 0.75, 1.0))))
) +
# Maps the Y-axis labels back to the KEGG pathway descriptions
scale_y_continuous(
breaks = plot_data_kegg$y_pos,
labels = plot_data_kegg$Description
) +
# Labels and Chart Title
labs(
title = "KEGG Pathway Enrichment Analysis",
x = "Gene count", # X-axis is now Gene Count
y = "KEGG Pathway" # Y-axis is the name of the pathway
) +
# Chart Theme and Style
theme_minimal() +
theme(
axis.text.y = element_text(size = 12, face = "bold"), # KEGG terms in bold and larger font
axis.title = element_text(size = 14, face = "bold"), # Axis titles
plot.title = element_text(size = 16, face = "bold", hjust = 0.5), # Centred title
legend.position = "right", # Position of subtitles
legend.title = element_text(size = 12, face = "bold"),
legend.text = element_text(size = 10),
panel.grid.major.y = element_blank(), # Remove standard horizontal grid lines
panel.grid.minor = element_blank(), # Remove smaller grid lines
panel.border = element_rect(colour = "black", fill=NA, linewidth=1.2) # Black border around the plot
)
} 
barplot(ekegg, showCategory = 10, title = "KEGG Enrichment Analysis")## Warning in fortify(object, showCategory = showCategory, by = x, ...): Arguments in `...` must be used.
## ✖ Problematic argument:
## • by = x
## ℹ Did you misspell an argument name?
# Network graph of enriched terms
cnetplot(ekegg, showCategory = 10)
# Heatmap
heatplot(ekegg, showCategory = 10)
9. Transcription factors between the analysis of AS vs Healthy
# Load the TxDb database
txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene
# Extraction of exons by gene
exons_by_gene <- exonsBy(txdb, by = "gene")
# Obtain the coordinates of the genes (taking the first and last positions of the exons)
genes_info <- range(exons_by_gene)
# Obtain transcription information
transcripts_info <- transcripts(txdb)
# Map genes of interest to Entrez IDs (replace “de_genes” with the actual list of genes)
gene_entrez <- mapIds(org.Hs.eg.db, keys = mapped_genes$Symbol, column = "ENTREZID", keytype = "SYMBOL", multiVals = "first")## 'select()' returned 1:1 mapping between keys and columns# Filter the genes of interest
promoters_info <- subset(genes_info, names(genes_info) %in% gene_entrez)
# Define promoter regions (2 kb upstream of TSS)
promoters <- promoters(promoters_info, upstream = 2000, downstream = 0)
# Filter the main chromosomes
promoters <- keepStandardChromosomes(promoters, pruning.mode = "coarse")
# Remove any regions that exceed the limits of the chromosomes.
promoters <- trim(promoters)
# Convert CompressedGRangesList promoters to GRanges
promoters_gr <- unlist(promoters)
# Load the JASPAR grounds database
motifs <- getMatrixSet(JASPAR2020, opts = list(species = "Homo sapiens"))
# Create a data frame with the IDs of the reasons and their names (TFs)
motif_info <- data.frame(
motif_id = names(motifs),
tf_name = sapply(motifs, function(x) x@name),
stringsAsFactors = FALSE
)
# Enriching motifs in promoting regions
motifHits <- matchMotifs(motifs, promoters_gr, genome = BSgenome.Hsapiens.UCSC.hg38)
# Count the number of occurrences of the reasons in each promoting region
motif_counts <- countOverlaps(promoters_gr, motifHits)
# Add counts to GRanges with promoting regions
promoters_gr$motif_counts <- motif_counts
# Summary of motif counts
summary(promoters_gr$motif_counts)## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 0.0000 0.0000 0.0000 0.4737 1.0000 1.0000# Obtain the names of the motifs and TFs
motif_names <- names(motifHits)
# Extract the reason table from the RangedSummarizedExperiment object
motif_data <- assays(motifHits)[[1]] # Assuming that the table of reasons is in the first list of assays
# Obtain information about TFs
# The names of the TFs can be in the colnames or in associated metadata
tf_names <- colnames(motif_data)
# Add the reason count if available
motif_counts <- rowSums(motif_data) # Count the occurrence of motifs (adjust as necessary)
# Check the dimensions of the motif_data object
dim(motif_data) # Number of rows and columns## [1] 19 633# Check the length of tf_names and motif_counts
tf_names_length <- length(tf_names)
motif_counts_length <- length(motif_counts)
# Print the lengths for diagnosis
cat("Length of tf_names:", tf_names_length, "\n")## Length of tf_names: 633cat("Length of motif_counts:", motif_counts_length, "\n")## Length of motif_counts: 19# Verify that the dimensions of motif_data correspond to the number of TFs and motifs
motif_data_dims <- dim(motif_data)
cat("Dimensions of motif_data (rows, columns):", motif_data_dims, "\n")## Dimensions of motif_data (rows, columns): 19 633# Check whether the number of reasons is greater or lesser
if (tf_names_length > motif_counts_length) {
# Check additional columns
tf_names <- tf_names[1:motif_counts_length] # Adjust to the length of motif_counts
} else {
# Adjust motif_counts to match tf_names
motif_counts <- motif_counts[1:tf_names_length]
}
# Now, I have created the data frame with adjusted lengths
motif_summary <- data.frame(
tf_name = tf_names,
motif_count = motif_counts
)
# Check the correspondence between TF names and the columns in motif_data
all(tf_names %in% colnames(motif_data)) # Should return TRUE if all TF names are present## [1] TRUE# Sort and identify key TFs
tf_summary <- motif_summary[order(motif_summary$motif_count, decreasing = TRUE), ]
top_tf_summary <- head(tf_summary, 130) # Adjust the number as required.
# Mapping Entrez IDs to gene symbols
gene_symbols <- mapIds(org.Hs.eg.db, keys = rownames(top_tf_summary), column = "SYMBOL", keytype = "ENTREZID", multiVals = "first")## 'select()' returned 1:1 mapping between keys and columns# Replace rownames with gene symbols
rownames(top_tf_summary) <- gene_symbols
top_tf_summary$motif_id <- rownames(top_tf_summary)
# Combine with the table of TF names
motif1 <- merge(top_tf_summary, motif_info, by.x = "tf_name", by.y = "motif_id")
# Reorganise columns for better viewing
motif2<- motif1[, c("motif_id", "tf_name.y", "motif_count")]
colnames(motif2) <- c("motif_id", "tf_name.y", "motif_count")
# View
print(motif2)## motif_id tf_name.y motif_count
## 1 GJB6 FOXF2 173
## 2 CCR6 FOXD1 103
## 3 CCR7 IRF2 206
## 4 DDIT3 MZF1(var.2) 139
## 5 FOS MAX::MYC 152
## 6 CXCL2 PPARG 182
## 7 IFNG PAX6 128
## 8 CXCL8 PBX1 218
## 9 JUN RORA 142
## 10 JUNB RORA(var.2) 118
## 11 AREG RREB1 182
## 12 MYC RXRA::VDR 153
## 13 PER1 SOX9 144
## 14 RORC SRY 170
## 15 CCL2 TAL1::TCF3 102
## 16 TNFAIP3 REL 198
## 17 ZFP36 RELA 126
## 18 FOSL1 NR1H2::RXRA 117
## 19 CD69 NFIC::TLX1 13710. Comparison between peripheral blood samples from AS patients and PsA patients.
# Wald test to obtain contrast-specific results
dsd <- DESeq(dsa, test = "Wald", sfType = "poscount")## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing## -- replacing outliers and refitting for 9 genes
## -- DESeq argument 'minReplicatesForReplace' = 7
## -- original counts are preserved in counts(dds)## estimating dispersions## fitting model and testingr <- results(dsd, contrast = c("Group", groups[2], groups[1]), alpha = 0.05, pAdjustMethod = "fdr")
groups <- levels(colData(dsd)$Group)
df <- as.data.frame(r)
# Filter only significant genes
sig_genes <- subset(r, padj < 0.05 & abs(log2FoldChange) >= 1)
# volcano plot
old.pal <- palette(c("#00BFFF", "#FF3030")) # low-hi colors
par(mar=c(4,4,2,1), cex.main=1.5)
with(sig_genes, {
plot(log2FoldChange, -log10(padj), main=paste(groups[2], "vs", groups[1]),
xlab="log2FC", ylab="-log10(Padj)", pch=20, cex=0.5)
text(log2FoldChange, -log10(padj), labels=rownames(r), cex=0.6, pos=4)
})
with(subset(r, padj<0.05 & abs(log2FoldChange) >= 1),
points(log2FoldChange, -log10(padj), pch=20, col=(sign(log2FoldChange) + 3)/2, cex=1))
legend("bottomleft", title=paste("Padj<", 0.05, sep=""), legend=c("down", "up"), pch=20,col=1:2)
# Plot only significant genes
# MD PLOT
par(mar=c(4,4,2,1), cex.main=1.5)
with(sig_genes, {
plot(log10(baseMean), log2FoldChange,
main=paste(groups[2], "vs", groups[1]),
xlab="log10(mean of normalized counts)", ylab="log2FoldChange",
pch=20, col=(sign(log2FoldChange) + 3)/2, cex=1)
text(log10(baseMean), log2FoldChange, labels=rownames(sig_genes), cex=0.6, pos=4)
})
legend("bottomleft", title=paste("Padj<", 0.05, sep=""), legend=c("down", "up"), pch=20, col=1:2)
abline(h=0)
palette(old.pal) # restore palette
# Add gene symbols to the points on the graph
# Install the packages if you do not already have them
library(ggplot2)
library(ggrepel)
plotVolcano <- function(res, title = "Volcano Plot") {
res$group <- "NS"
res$group[res$padj < 0.05 & res$log2FoldChange > 1] <- "Up"
res$group[res$padj < 0.05 & res$log2FoldChange < -1] <- "Down"
res$label <- ifelse(res$group != "NS", rownames(res), NA)
ggplot(res, aes(x = log2FoldChange, y = -log10(padj), color = group)) +
geom_point(alpha = 0.7, size = 2) +
geom_hline(yintercept = -log10(0.05), linetype = "dashed") +
geom_vline(xintercept = c(-1, 1), linetype = "dashed") +
scale_color_manual(values = c("Up" = "firebrick", "Down" = "dodgerblue", "NS" = "grey80")) +
ggrepel::geom_text_repel(aes(label = label), size = 3, max.overlaps = Inf) +
theme_minimal() +
labs(title = title, x = "log2 Fold Change", y = "-log10 adjusted p-value", color = "Regulation")
}
# Example of function usage
plotVolcano(r, paste(groups[2], "vs", groups[1]))## Warning: Removed 78 rows containing missing values or values outside the scale range
## (`geom_point()`).## Warning: Removed 424 rows containing missing values or values outside the scale range
## (`geom_text_repel()`).
# Genes upregulated
up_genes <- rownames(subset(r, padj < 0.05 & log2FoldChange >= 1))
# Genes downregulated
down_genes <- rownames(subset(r, padj < 0.05 & log2FoldChange <= -1))
# All DEGs with |log2FC| > 2
de_genes <- c(up_genes, down_genes)
expr_datasa <- as.data.frame(expr_data[rownames(expr_data) %in% de_genes, ])
# Convert expression data to long format for ggplot2
expr_datas <- as.data.frame(expr_datasa)
expr_datas$Gene <- rownames(expr_datas)
expr_datas <- pivot_longer(expr_datas, cols = -Gene, names_to = "Sample", values_to = "Expression")
expr_datas <- merge(expr_datas, pheno_data, by.x = "Sample", by.y = "geo_accession")
# Check column names and a sample of the data
expresse <- r[order(r$padj)[1:429], ]
expresse <- merge(as.data.frame(expresse), expr_datasa, by = 0, sort = F)
library(dplyr)
library(tibble)
library(clusterProfiler)
library(ggplot2)
r_df <- as.data.frame(r)
# Assuming that “r_df” is your data frame with the DESeq2 results
# This ensures that gene names are preserved.
r_df_com_genes <- r_df %>%
rownames_to_column(var = "Gene")
top30_fc <- r_df_com_genes %>%
dplyr::filter(padj < 0.05 & abs(log2FoldChange) > 1) %>%
dplyr::arrange(desc(abs(log2FoldChange))) %>%
dplyr::slice(1:30) %>%
dplyr::mutate(
Regulation = case_when(
log2FoldChange > 1 ~ "Upregulated",
log2FoldChange < -1 ~ "Downregulated"
)
)
# Chart with positive and negative bars
ggplot(top30_fc, aes(x = reorder(Gene, log2FoldChange), y = log2FoldChange, fill = Regulation)) +
geom_col() +
coord_flip() + # Place the genes on the Y axis
scale_fill_manual(values = c("Upregulated" = "steelblue", "Downregulated" = "tomato")) +
scale_y_continuous(breaks = seq(-8, 4, by = 1)) + # Adjust the limits if necessary.
theme_bw() +
labs(
title = "The most prominent DEGs between AS and PsA (GSE117769)",
x = "Gene",
y = "log2 Fold Change",
fill = "Regulation"
) +
theme(
axis.text.y = element_text(color = "black", face = "bold", size = 9)
)
# --- Selects the 20 MOST overexpressed genes ---
up_20genes <- expresse %>%
filter(padj < 0.05 & log2FoldChange > 1) %>%
arrange(desc(log2FoldChange)) %>%
head(20) %>%
pull(Row.names)
# --- Filters expression data ---
expr_datas_filtrado_up <- expr_datas %>%
filter(`characteristics_ch1.6` %in% c("phenotype: Ankylosing spondylitis", "phenotype: Psoriatic arthritis")) %>%
filter(Gene %in% up_20genes)
# --- Calculates the average per gene and per group ---
expr_datasa_up <- expr_datas_filtrado_up %>%
group_by(Gene, `characteristics_ch1.6`) %>%
summarise(
mean_expression = mean(Expression, na.rm = TRUE),
sd_expression = sd(Expression, na.rm = TRUE),
.groups = 'drop'
)
# --- Preparation for the chart ---
# Filter to show the average expression ONLY in the “non-lesion” group
dados_para_plotar_up <- expr_datasa_up %>%
filter(characteristics_ch1.6 == "phenotype: Ankylosing spondylitis")
# --- Graph Generation ---
ggplot(dados_para_plotar_up, aes(x = mean_expression, y = reorder(Gene, mean_expression))) +
geom_col(fill = "steelblue", color = "black", width = 0.7) +
labs(
title = "Average Expression of the Main Upregulated Genes in Ankylosing spondylitis", # Título mais claro
subtitle = "For AS vs PsA (GSE117769)",
x = "Average Expression in the Group 'AS'", # Rótulo do eixo mais claro
y = "Gene"
) +
theme_minimal(base_size = 14) +
theme(
panel.grid.major.y = element_blank(),
axis.text.y = element_text(size = 12)
)
# --- Selects the 20 MOST under-expressed genes ---
down_20genes <- expresse %>%
filter(padj < 0.05 & log2FoldChange < -1) %>%
arrange(log2FoldChange) %>% # <-- Sort from most negative to least negative
head(20) %>%
pull(Row.names)
# --- Filters expression data for genes and groups of interest ---
expr_datas_filtrado_down <- expr_datas %>%
filter(`characteristics_ch1.6` %in% c("phenotype: Ankylosing spondylitis", "phenotype: Psoriatic arthritis")) %>%
filter(Gene %in% down_20genes)
# --- Calculates the average per gene and per group ---
expr_datasa_down <- expr_datas_filtrado_down %>%
group_by(Gene, `characteristics_ch1.6`) %>%
summarise(
mean_expression = mean(Expression, na.rm = TRUE),
.groups = 'drop'
)
# --- Preparation for the chart ---
# Filter to show the average expression ONLY in the “lesion” group
dados_para_plotar <- expr_datasa_down %>%
filter(characteristics_ch1.6 == "phenotype: Ankylosing spondylitis")
# --- Graph Generation ---
ggplot(dados_para_plotar, aes(x = mean_expression, y = reorder(Gene, -mean_expression))) +
geom_col(fill = "red", color = "black", width = 0.7) +
labs(
title = "Average Expression of the Main Downregulated Genes in Ankylosing spondylitis", # Título mais claro
subtitle = "For AS vs PsA (GSE117769)",
x = "Average Expression in the Group 'AS'", # Rótulo do eixo mais claro
y = "Gene"
) +
theme_minimal(base_size = 14) +
theme(
panel.grid.major.y = element_blank(),
axis.text.y = element_text(size = 12)
)
# --- The code to create 'count_array' ---
up_genes <- rownames(subset(r, padj < 0.05 & log2FoldChange > 1))
down_genes <- rownames(subset(r, padj < 0.05 & log2FoldChange < -1))
genes_interesse <- c(up_genes, down_genes)
expr_filtrado <- expr_datas %>%
filter(`characteristics_ch1.6` %in% c("phenotype: Ankylosing spondylitis", "phenotype: Psoriatic arthritis")) %>%
filter(Gene %in% genes_interesse)
matriz_contagem <- expr_filtrado %>%
select(Gene, Sample, Expression) %>%
pivot_wider(names_from = Sample, values_from = Expression, values_fill = 0) %>%
column_to_rownames(var = "Gene")
# Filter your original “sample_info” object to keep only the samples that are in your final matrix
# This ensures that the annotation corresponds exactly to the heatmap data
sample_info_filtrado <- subset(sample_info, rownames(sample_info) %in% colnames(matriz_contagem))
# Select the 20 most highly expressed genes
media_dos_genes <- rowMeans(matriz_contagem)
media_ordenada <- sort(media_dos_genes, decreasing = TRUE)
top_20_genes_por_media <- names(head(media_ordenada, 20))
heatmapData_top20 <- as.matrix(matriz_contagem[top_20_genes_por_media, ])
# Create the annotation for the heatmap from the filtered and corrected information
annotation_data <- data.frame(
Group = sample_info_filtrado$Group,
row.names = rownames(sample_info_filtrado)
)
# Ensure that the order of the columns in the heatmap and annotation is the same
heatmapData_top20 <- heatmapData_top20[, rownames(annotation_data)]
# --- Heatmap generation with ComplexHeatmap ---
# Rescale data by row (Z-score)
mat_scaled <- t(scale(t(heatmapData_top20)))
# Create the column annotation
ha_col <- HeatmapAnnotation(
Group = annotation_data$Group,
col = list(Group = c("AS" = "#1f77b4", "PsA" = "yellow"))
)
# Define the colour palette
cores <- colorRamp2(c(-2, 0, 2), rev(RColorBrewer::brewer.pal(3, "RdBu")))
# Generate the heatmap
Heatmap(
mat_scaled,
name = "Z-score",
top_annotation = ha_col,
col = cores,
# Divide the columns into groups for clearer viewing
column_split = annotation_data$Group,
cluster_rows = TRUE,
cluster_columns = TRUE, # Cluster within each divided group
show_column_names = FALSE,
show_row_names = TRUE,
column_title = "Heatmap of the most highly expressed DEGs (AS vs. PsA GSE117769)",
heatmap_legend_param = list(title = "Z-score")
)
# Filter differentially expressed genes
de_genes <- subset(r, padj < 0.05 & abs(log2FoldChange) > 1)
#Create a data frame from de_genes
de_genes <- data.frame(de_genes)
# Suppose your dataframe is called df and you want to select columns ‘column1’, “column2” and ‘column3’
de_genes <- de_genes %>% select(log2FoldChange, padj)
# Assuming that rownames(df) are gene symbols
gene_symbols <- rownames(de_genes)
# Convert gene symbols to Entrez IDs
gene_entrez_ids <- bitr(gene_symbols, fromType = "SYMBOL", toType = "ENTREZID", OrgDb = org.Hs.eg.db)## 'select()' returned 1:1 mapping between keys and columns# First, convert the rownames from df into a column
de_genes$Symbol <- rownames(de_genes)
# Performs the join between the original table and the converted IDs
de_genes <- merge(de_genes, gene_entrez_ids, by.x = "Symbol", by.y = "SYMBOL", all.x = TRUE)
# Ensure unique symbols
de_genes <- de_genes[!duplicated(de_genes$ENTREZID), ]
# Alternative Workflow with STRINGdb Integration in R
# Initialise the STRINGdb object for a specific organism
string_db <- STRINGdb$new(version = "12", species = 9606, score_threshold = 400, input_directory = "")
options(timeout = 600) # increases to 10 minutes
# Gene mapping using STRINGdb
mapped_genes <- string_db$map(de_genes, "Symbol", removeUnmappedRows = TRUE)
# Recover interactions for mapped genes
interactions <- string_db$get_interactions(mapped_genes$STRING_id)
# Visualise the network using igraph or other visualisation tools
library(igraph)
g <- graph_from_data_frame(interactions, directed=FALSE)
plot(g)
# Detect clusters (e.g. Louvain)
clusters <- cluster_louvain(g)
# Plot with colours by cluster
plot(g, vertex.color=clusters$membership)
# Perform GO enrichment analysis
# Biological Process
enrich_result <- enrichGO(gene = mapped_genes$Symbol,
OrgDb = org.Hs.eg.db,
keyType = "SYMBOL",
ont = "BP", # Biological Ontology. It can be ‘BP’, “MF”, or ‘CC’.
pAdjustMethod = "BH",
pvalueCutoff = 0.05,
qvalueCutoff = 0.2)
barplot(enrich_result, showCategory = 10, title= "GO Enrichment Analysis")## Warning in fortify(object, showCategory = showCategory, by = x, ...): Arguments in `...` must be used.
## ✖ Problematic argument:
## • by = x
## ℹ Did you misspell an argument name?
# Network graph of enriched terms
cnetplot(enrich_result, showCategory = 10)
# Heatmap
heatplot(enrich_result, showCategory = 10)
11. Transcription factors between the analysis of AS vs PsA.
# Load the TxDb database
txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene
# Extraction of exons by gene
exons_by_gene <- exonsBy(txdb, by = "gene")
# Obtain the coordinates of the genes (taking the first and last positions of the exons)
genes_info <- range(exons_by_gene)
# Obtain transcription information
transcripts_info <- transcripts(txdb)
# Map genes of interest to Entrez IDs (replace “de_genes” with the actual list of genes)
gene_entrez <- mapIds(org.Hs.eg.db, keys = mapped_genes$Symbol, column = "ENTREZID", keytype = "SYMBOL", multiVals = "first")## 'select()' returned 1:1 mapping between keys and columns# Filter the genes of interest
promoters_info <- subset(genes_info, names(genes_info) %in% gene_entrez)
# Define promoter regions (2 kb upstream of TSS)
promoters <- promoters(promoters_info, upstream = 2000, downstream = 0)
# Filter the main chromosomes
promoters <- keepStandardChromosomes(promoters, pruning.mode = "coarse")
# Remove any regions that exceed the limits of the chromosomes.
promoters <- trim(promoters)
# Convert CompressedGRangesList promoters to GRanges
promoters_gr <- unlist(promoters)
# Load the JASPAR grounds database
motifs <- getMatrixSet(JASPAR2020, opts = list(species = "Homo sapiens"))
# Create a data frame with the IDs of the reasons and their names (TFs)
motif_info <- data.frame(
motif_id = names(motifs),
tf_name = sapply(motifs, function(x) x@name),
stringsAsFactors = FALSE
)
# Enriching motifs in promoting regions
motifHits <- matchMotifs(motifs, promoters_gr, genome = BSgenome.Hsapiens.UCSC.hg38)
# Count the number of occurrences of the reasons in each promoting region
motif_counts <- countOverlaps(promoters_gr, motifHits)
# Add counts to GRanges with promoting regions
promoters_gr$motif_counts <- motif_counts
# Summary of motif counts
summary(promoters_gr$motif_counts)## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 1 1 1 1 1 1# Obtain the names of the motifs and TFs
motif_names <- names(motifHits)
# Extract the reason table from the RangedSummarizedExperiment object
motif_data <- assays(motifHits)[[1]] # Assuming that the table of reasons is in the first list of assays
# Obtain information about TFs
# The names of the TFs can be in the colnames or in associated metadata
tf_names <- colnames(motif_data)
# Add the reason count if available
motif_counts <- rowSums(motif_data) # Count the occurrence of motifs (adjust as necessary)
# Check the dimensions of the motif_data object
dim(motif_data) # Number of rows and columns## [1] 4 633# Check the length of tf_names and motif_counts
tf_names_length <- length(tf_names)
motif_counts_length <- length(motif_counts)
# Print the lengths for diagnosis
cat("Length of tf_names:", tf_names_length, "\n")## Length of tf_names: 633cat("Length of motif_counts:", motif_counts_length, "\n")## Length of motif_counts: 4# Verify that the dimensions of motif_data correspond to the number of TFs and motifs
motif_data_dims <- dim(motif_data)
cat("Dimensions of motif_data (rows, columns):", motif_data_dims, "\n")## Dimensions of motif_data (rows, columns): 4 633# Check whether the number of reasons is greater or lesser
if (tf_names_length > motif_counts_length) {
# Check additional columns
tf_names <- tf_names[1:motif_counts_length] # Adjust to the length of motif_counts
} else {
# Adjust motif_counts to match tf_names
motif_counts <- motif_counts[1:tf_names_length]
}
# Now, I have created the data frame with adjusted lengths
motif_summary <- data.frame(
tf_name = tf_names,
motif_count = motif_counts
)
# Check the correspondence between TF names and the columns in motif_data
all(tf_names %in% colnames(motif_data)) # Should return TRUE if all TF names are present## [1] TRUE# Sort and identify key TFs
tf_summary <- motif_summary[order(motif_summary$motif_count, decreasing = TRUE), ]
top_tf_summary <- head(tf_summary, 130) # Adjust the number as required.
# Mapping Entrez IDs to gene symbols
gene_symbols <- mapIds(org.Hs.eg.db, keys = rownames(top_tf_summary), column = "SYMBOL", keytype = "ENTREZID", multiVals = "first")## 'select()' returned 1:1 mapping between keys and columns# Replace rownames with gene symbols
rownames(top_tf_summary) <- gene_symbols
top_tf_summary$motif_id <- rownames(top_tf_summary)
# Combine with the table of TF names
motif1 <- merge(top_tf_summary, motif_info, by.x = "tf_name", by.y = "motif_id")
# Reorganise columns for better viewing
motif2<- motif1[, c("motif_id", "tf_name.y", "motif_count")]
colnames(motif2) <- c("motif_id", "tf_name.y", "motif_count")
# View
print(motif2)## motif_id tf_name.y motif_count
## 1 CCR6 FOXF2 100
## 2 CLEC4D FOXD1 107
## 3 MMP9 IRF2 180
## 4 RETN MZF1(var.2) 111